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Sample records for fuzzy tandem repeats

  1. TRStalker: an efficient heuristic for finding fuzzy tandem repeats

    PubMed Central

    Pellegrini, Marco; Renda, M. Elena; Vecchio, Alessio

    2010-01-01

    Motivation: Genomes in higher eukaryotic organisms contain a substantial amount of repeated sequences. Tandem Repeats (TRs) constitute a large class of repetitive sequences that are originated via phenomena such as replication slippage and are characterized by close spatial contiguity. They play an important role in several molecular regulatory mechanisms, and also in several diseases (e.g. in the group of trinucleotide repeat disorders). While for TRs with a low or medium level of divergence the current methods are rather effective, the problem of detecting TRs with higher divergence (fuzzy TRs) is still open. The detection of fuzzy TRs is propaedeutic to enriching our view of their role in regulatory mechanisms and diseases. Fuzzy TRs are also important as tools to shed light on the evolutionary history of the genome, where higher divergence correlates with more remote duplication events. Results: We have developed an algorithm (christened TRStalker) with the aim of detecting efficiently TRs that are hard to detect because of their inherent fuzziness, due to high levels of base substitutions, insertions and deletions. To attain this goal, we developed heuristics to solve a Steiner version of the problem for which the fuzziness is measured with respect to a motif string not necessarily present in the input string. This problem is akin to the ‘generalized median string’ that is known to be an NP-hard problem. Experiments with both synthetic and biological sequences demonstrate that our method performs better than current state of the art for fuzzy TRs and that the fuzzy TRs of the type we detect are indeed present in important biological sequences. Availability: TRStalker will be integrated in the web-based TRs Discovery Service (TReaDS) at bioalgo.iit.cnr.it. Contact: marco.pellegrini@iit.cnr.it Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20529928

  2. Ab initio detection of fuzzy amino acid tandem repeats in protein sequences

    PubMed Central

    2012-01-01

    Background Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats). Results In this paper we present PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that PTRStalker can detect global symmetries in the primary structure which are then reflected in the tertiary structure. Conclusions PTRStalker is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available. PMID:22536906

  3. Short Tandem Repeat DNA Internet Database

    National Institute of Standards and Technology Data Gateway

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  4. Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases

    PubMed Central

    2012-01-01

    Background Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters. Results In this paper we present TReaDS - Tandem Repeats Discovery Service, a tandem repeat meta search engine. TReaDS forwards user requests to several state of the art tools for finding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, TReaDS allows the user to (i) simultaneously run different algorithms on the same data set, (ii) choose for each algorithm a different setting of parameters, and (iii) obtain a report that can be downloaded for further, off-line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases. Conclusions By using the tool TReaDS we discover that, for 27 repeat expansion diseases out of a currently known set of 29, long fuzzy tandem repeats are covering the expansion loci. Tests with control sets confirm the specificity of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability. We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our

  5. RepeatsDB: a database of tandem repeat protein structures

    PubMed Central

    Di Domenico, Tomás; Potenza, Emilio; Walsh, Ian; Gonzalo Parra, R.; Giollo, Manuel; Minervini, Giovanni; Piovesan, Damiano; Ihsan, Awais; Ferrari, Carlo; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2014-01-01

    RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services. PMID:24311564

  6. Nucleic acid recognition by tandem helical repeats.

    PubMed

    Rubinson, Emily H; Eichman, Brandt F

    2012-02-01

    Protein domains constructed from tandem α-helical repeats have until recently been primarily associated with protein scaffolds or RNA recognition. Recent crystal structures of human mitochondrial termination factor MTERF1 and Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA revealed two new superhelical tandem repeat architectures capable of wrapping around the double helix in unique ways. Unlike DNA sequence recognition motifs that rely mainly on major groove read-out, MTERF and ALK motifs locate target sequences and aberrant nucleotides within DNA by resculpting the double-helix through extensive backbone contacts. Comparisons between MTERF and ALK repeats, together with recent advances in ssRNA recognition by Pumilio/FBF (PUF) domains, provide new insights into the fundamental principles of protein-nucleic acid recognition. PMID:22154606

  7. [Tandem repeats in rodents genome and their mapping].

    PubMed

    Ostromyshenskii, D I; Kuznetsova, L S; Komissarov, A S; Kartavtseva, I V; Podgornaya, L

    2015-01-01

    Tandemly-repeated sequences represent a unique class of eukaryotic DNA. Their content in the genome of higher eukaryotes mounts to tens of percents. However, the evolution of this class of sequences is poorly-studied. In our paper, 62 families of Mus musculus tandem repeats are analyzed by bioinformatic methods, and 7 of them are analyzed by fluorescence in situ hybridization. It is shown that the same tandem repeat sets co-occure only in closely related species of mice. But even in such species we observe differences in localization on the chromosomes and the number of individual tandem repeats. With increasing evolutionary distance only some of the tandem repeat families remain common for different species. It is shown, that the use of a combination of bioinformatics and molecular biology techniques is very perspective for further studies of the evolution of tandem repeats. PMID:26035967

  8. Intragenic tandem repeat variation between Legionella pneumophila strains

    PubMed Central

    Coil, David A; Vandersmissen, Liesbeth; Ginevra, Christophe; Jarraud, Sophie; Lammertyn, Elke; Anné, Jozef

    2008-01-01

    Background Bacterial genomes harbour a large number of tandem repeats, yet the possible phenotypic effects of those found within the coding region of genes are only beginning to be examined. Evidence exists from other organisms that these repeats can be involved in the evolution of new genes, gene regulation, adaptation, resistance to environmental stresses, and avoidance of the immune system. Results In this study, we have investigated the presence and variability in copy number of intragenic tandemly repeated sequences in the genome of Legionella pneumophila, the etiological agent of a severe pneumonia known as Legionnaires' disease. Within the genome of the Philadelphia strain, we have identified 26 intragenic tandem repeat sequences using conservative selection criteria. Of these, seven were "polymorphic" in terms of repeat copy number between a large number of L. pneumophila serogroup 1 strains. These strains were collected from a wide variety of environments and patients in several geographical regions. Within this panel of strains, all but one of these seven genes exhibited statistically different patterns in repeat copy number between samples from different origins (environmental, clinical, and hot springs). Conclusion These results support the hypothesis that intragenic tandem repeats could play a role in virulence and adaptation to different environments. While tandem repeats are an increasingly popular focus of molecular typing studies in prokaryotes, including in L. pneumophila, this study is the first examining the difference in tandem repeat distribution as a function of clinical or environmental origin. PMID:19077205

  9. NTRFinder: a software tool to find nested tandem repeats.

    PubMed

    Matroud, Atheer A; Hendy, M D; Tuffley, C P

    2012-02-01

    We introduce the software tool NTRFinder to search for a complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that NTRs can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real NTRs of interest. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/~aamatroud/. PMID:22121222

  10. Tandem repeat distribution of gene transcripts in three plant families

    PubMed Central

    2009-01-01

    Tandem repeats (microsatellites or SSRs) are molecular markers with great potential for plant genetic studies. Modern strategies include the transfer of these markers among widely studied and orphan species. In silico analyses allow for studying distribution patterns of microsatellites and predicting which motifs would be more amenable to interspecies transfer. Transcribed sequences (Unigene) from ten species of three plant families were surveyed for the occurrence of micro and minisatellites. Transcripts from different species displayed different rates of tandem repeat occurrence, ranging from 1.47% to 11.28%. Both similar and different patterns were found within and among plant families. The results also indicate a lack of association between genome size and tandem repeat fractions in expressed regions. The conservation of motifs among species and its implication on genome evolution and dynamics are discussed. PMID:21637460

  11. Tandem-repeat protein domains across the tree of life

    PubMed Central

    Jernigan, Kristin K.

    2015-01-01

    Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. PMID:25653910

  12. Fully integrated, fully automated generation of short tandem repeat profiles

    PubMed Central

    2013-01-01

    Background The generation of short tandem repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short tandem repeat profiles from buccal swab samples, to improve forensic laboratory process flow as well as to enable short tandem repeat profile generation to be performed in police stations and in field-forward military, intelligence, and homeland security settings. Results An integrated system was developed consisting of an injection-molded microfluidic BioChipSet cassette, a ruggedized instrument, and expert system software. For each of five buccal swabs, the system purifies DNA using guanidinium-based lysis and silica binding, amplifies 15 short tandem repeat loci and the amelogenin locus, electrophoretically separates the resulting amplicons, and generates a profile. No operator processing of the samples is required, and the time from swab insertion to profile generation is 84 minutes. All required reagents are contained within the BioChipSet cassette; these consist of a lyophilized polymerase chain reaction mix and liquids for purification and electrophoretic separation. Profiles obtained from fully automated runs demonstrate that the integrated system generates concordant short tandem repeat profiles. The system exhibits single-base resolution from 100 to greater than 500 bases, with inter-run precision with a standard deviation of ±0.05 - 0.10 bases for most alleles. The reagents are stable for at least 6 months at 22°C, and the instrument has been designed and tested to Military Standard 810F for shock and vibration ruggedization. A nontechnical user can operate the system within or outside the laboratory. Conclusions The integrated system represents the

  13. Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

    PubMed

    Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

    1997-12-01

    Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R. PMID:9451957

  14. Versatile communication strategies among tandem WW domain repeats

    PubMed Central

    Dodson, Emma Joy; Fishbain-Yoskovitz, Vered; Rotem-Bamberger, Shahar

    2015-01-01

    Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands. PMID:25710931

  15. Tandemly repeated DNA families in the mouse genome

    PubMed Central

    2011-01-01

    Background Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies. Results Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites. To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions. Conclusions Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report

  16. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role.

    PubMed

    Pellegrini, Marco

    2015-01-01

    Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR. PMID:26442257

  17. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

    PubMed Central

    Pellegrini, Marco

    2015-01-01

    Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR. PMID:26442257

  18. Evolutionary Footprints of Short Tandem Repeats in Avian Promoters

    PubMed Central

    Abe, Hideaki; Gemmell, Neil J.

    2016-01-01

    Short tandem repeats (STRs) or microsatellites are well-known sequence elements that may change the spacing between transcription factor binding sites (TFBSs) in promoter regions by expansion or contraction of repetitive units. Some of these mutations have the potential to contribute to phenotypic diversity by altering patterns of gene expression. To explore how repetitive sequence motifs within promoters have evolved in avian lineages under mutation-selection balance, more than 400 evolutionary conserved STRs (ecSTRs) were identified in this study by comparing the 2 kb upstream promoter sequences of chicken against those of other birds (turkey, duck, zebra finch, and flycatcher). The rate of conservation was significantly higher in AG dinucleotide repeats than in AC or AT repeats, with the expansion of AG motifs being noticeably constrained in passerines. Analysis of the relative distance between ecSTRs and TFBSs revealed a significantly higher rate of conserved TFBSs in the vicinity of ecSTRs in both chicken-duck and chicken-passerine comparisons. Our comparative study provides a novel insight into which intrinsic factors have influenced the degree of constraint on repeat expansion/contraction during avian promoter evolution. PMID:26766026

  19. An efficient clustering algorithm for partitioning Y-short tandem repeats data

    PubMed Central

    2012-01-01

    Background Y-Short Tandem Repeats (Y-STR) data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results. Results Our new algorithm, called k-Approximate Modal Haplotypes (k-AMH), obtains the highest clustering accuracy scores for five out of six datasets, and produces an equal performance for the remaining dataset. Furthermore, clustering accuracy scores of 100% are achieved for two of the datasets. The k-AMH algorithm records the highest mean accuracy score of 0.93 overall, compared to that of other algorithms: k-Population (0.91), k-Modes-RVF (0.81), New Fuzzy k-Modes (0.80), k-Modes (0.76), k-Modes-Hybrid 1 (0.76), k-Modes-Hybrid 2 (0.75), Fuzzy k-Modes (0.74), and k-Modes-UAVM (0.70). Conclusions The partitioning performance of the k-AMH algorithm for Y-STR data is superior to that of other algorithms, owing to its ability to solve the non-unique centroids and local minima problems. Our algorithm is also efficient in terms of time complexity, which is recorded as O(km(n-k)) and considered to be linear. PMID:23039132

  20. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

    PubMed Central

    2013-01-01

    Background Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Results Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. Conclusions While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes. PMID:23363705

  1. The role of variable DNA tandem repeats in bacterial adaptation.

    PubMed

    Zhou, Kai; Aertsen, Abram; Michiels, Chris W

    2014-01-01

    DNA tandem repeats (TRs), also designated as satellite DNA, are inter- or intragenic nucleotide sequences that are repeated two or more times in a head-to-tail manner. Because TR tracts are prone to strand-slippage replication and recombination events that cause the TR copy number to increase or decrease, loci containing TRs are hypermutable. An increasing number of examples illustrate that bacteria can exploit this instability of TRs to reversibly shut down or modulate the function of specific genes, allowing them to adapt to changing environments on short evolutionary time scales without an increased overall mutation rate. In this review, we discuss the prevalence and distribution of inter- and intragenic TRs in bacteria and the mechanisms of their instability. In addition, we review evidence demonstrating a role of TR variations in bacterial adaptation strategies, ranging from immune evasion and tissue tropism to the modulation of environmental stress tolerance. Nevertheless, while bioinformatic analysis reveals that most bacterial genomes contain a few up to several dozens of intra- and intergenic TRs, only a small fraction of these have been functionally studied to date. PMID:23927439

  2. The evolution and function of protein tandem repeats in plants.

    PubMed

    Schaper, Elke; Anisimova, Maria

    2015-04-01

    Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens. PMID:25420631

  3. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres comprise of megabase-scale arrays of tandem repeats. The true prevalence of centromere tandem repeats, and whether they exhibit conserved seque...

  4. Condensin Promotes Position Effects within Tandem DNA Repeats via the RITS complex

    PubMed Central

    He, Haijin; Zhang, Shu; Wang, Danni; Hochwagen, Andreas; Li, Fei

    2016-01-01

    Summary Tandem repetitive DNA is highly abundant in eukaryotic genomes, and contributes to transcription control and genome stability. However, how the individual sequences within tandem repeats behave remains largely unknown. Here we develop a collection of fission yeast strains with a reporter gene inserted at different units in a tandem repeat array. We show that, contrary to what is usually assumed, transcriptional silencing and replication timing among the individual repeats differ significantly. RNAi-mediated H3K9 methylation is essential for the silencing position effect. A short hairpin RNA of ura4+ induces silencing in trans within the tandem array in a position-dependent manner. Importantly, the position effect depends on the condensin subunit, cut3+. Cut3 promotes the position effect via interaction with the RNA-induced transcriptional silencing (RITS) complex. This study reveals variations in silencing within tandem DNA repeats and provides mechanistic insights into how DNA repeats at the individual level are regulated. PMID:26832414

  5. Tandem repeat knockout utilizing the CRISPR/Cas9 system in human cells.

    PubMed

    Lv, Qingyan; Lai, Liangxue; Yuan, Lin; Song, Yuning; Sui, Tingting; Li, Zhanjun

    2016-05-15

    Tandem repeats have been shown to cause human genetic diseases and contribute significantly to genome variation and instability. Although multi-sgRNAs mediated CRISPR/Cas9 system have used to generate regional deletions previously, in this study we explored a method of generating regional deletions of tandem repeats by taking advantage of the off-target effects of CRISPR/Cas9 in 293FT cells. Our results revealed that generation of large-fragment deletions of tandem repeats located in the MAGEL2 and XIST gene was possible. In summary, we have demonstrated that large-fragment deletions of tandem repeats can be achieved using a sgRNA-directed CRISPR/Cas9 system, facilitating the functional study of tandem repeats in future studies. PMID:26873114

  6. [Polymorphic loci and polymorphism analysis of short tandem repeats within XNP gene].

    PubMed

    Liu, Qi-Ji; Gong, Yao-Qin; Guo, Chen-Hong; Chen, Bing-Xi; Li, Jiang-Xia; Guo, Yi-Shou

    2002-01-01

    To select polymorphic short tandem repeat markers within X-linked nuclear protein (XNP) gene, genomic clones which contain XNP gene were recognized by homologous analysis with XNP cDNA. By comparing the cDNA with genomic DNA, non-exonic sequences were identified, and short tandem repeats were selected from non-exonic sequences by using BCM search Launcher. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. Five short tandem repeats were identified from XNP gene, two of which were polymorphic. Four and 11 alleles were observed in Chinese population for XNPSTR1 and XNPSTR4, respectively. Heterozygosities were 47% for XNPSTR1 and 70% for XNPSTR4. XNPSTR1 and XNPSTR4 localized within 3' end and intron 10, respectively. Two polymorphic short tandem repeats have been identified within XNP gene and will be useful for linkage analysis and gene diagnosis of XNP gene. PMID:12182071

  7. Distribution of repeat unit differences between alleles at tandem repeat microsatellite loci

    SciTech Connect

    Jin, L. |; Zhong, Y.; Chakraborty, R.

    1994-09-01

    PCR-based assays of tandemly repeated microsatellite loci detect genetic variation from which alleles may be scored by their repeat unit lengths. Comparison of allele sizes from such data yields a probability distribution (P{sub k}) of repeat unit differences (k) between alleles segregating in a population. We show that this distribution (P{sub k}; k = 0, 1,2,...) provides insight regarding the mechanism of production of new alleles at such loci and the demographic history of populations, far better than that obtained from other summary measures (e.g., heterozygosity, number of alleles, and the range of allele sizes). The distributions of P{sub k} under multi-step stepwise models of mutation are analytically derived, which show that when a population is at equilibrium under the mutation-drift balance, the distribution of repeat unit differences between alleles is positively skewed with a mode larger than zero. However, when the heterozygosity at a locus is low (say, less than 40%), P{sub k} is a monotonically decreasing function of k. Applications of this theory to data on repeat unit sizes at over 1,240 microsatellite loci from the Caucasians, categorized by the average heterozygosity of loci, indicate that at most microsatellite loci new alleles are produced by stepwise mutations, and this is consistent with the replication slippage mechanism of mutations. The repeat size changes of mutants are probably within one or two units of alleles from which the mutants arise. Distributions of P{sub k} at microsatellite loci located within genes show evidence of allele size constraints. No significant evidence of recent expansion of population sizes in the Caucasians is detected by the distribution of P{sub k}.

  8. Microchip-based forensic short tandem repeat genotyping.

    PubMed

    Kim, Yong Tae; Heo, Hyun Young; Oh, Shin Hye; Lee, Seung Hwan; Kim, Do Hyun; Seo, Tae Seok

    2015-08-01

    Micro total analysis system (μTAS) or lab-on-a-chip (LOC) technology has advanced over decades, and the high performance for chemical and biological analysis has been well demonstrated with advantages of low sample consumption, rapid analysis time, high-throughput screening, and portability. In particular, μTAS or LOC based genetic applications have been extensively explored, and the short tandem repeat (STR) typing on a chip has garnered attention in the forensic community due to its special use for human identification in the field of mass disaster and missing person investigation, paternity testing, and perpetrator identification. The STR typing process consists of sample collection, DNA extraction, DNA quantitation, STR loci amplification, capillary electrophoretic separation, and STR profiling. Recent progress of microtechnology shows its ability to substitute the conventional analytical tools, and furthermore demonstrates total integration of the whole STR processes on a single wafer for on-site STR typing. In this review article, we highlighted some representative results for fluorescence labeling techniques, microchip-based DNA purification, on-chip polymerase chain reaction (PCR), a capillary electrophoretic microdevice, and a fully integrated microdevice for STR typing. PMID:25963560

  9. Analysis of the largest tandemly repeated DNA families in the human genome

    PubMed Central

    Warburton, Peter E; Hasson, Dan; Guillem, Flavia; Lescale, Chloe; Jin, Xiaoping; Abrusan, Gyorgy

    2008-01-01

    Background Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence. Results Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families. Conclusion This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families. PMID:18992157

  10. Bovine gall-bladder mucin contains two distinct tandem repeating sequences: evidence for scavenger receptor cysteine-rich repeats.

    PubMed Central

    Nunes, D P; Keates, A C; Afdhal, N H; Offner, G D

    1995-01-01

    Gall-bladder mucin is a densely glycosylated macromolecule which is the primary secretory product of the gall-bladder epithelium. It has been shown to bind cholesterol and other biliary lipids and to promote cholesterol crystal nucleation in vitro. In order to understand the molecular basis for mucin-lipid interactions, bovine gall-bladder mucin cDNAs were identified by expression cloning and were isolated and sequenced. The nucleotide sequences of these cDNAs revealed two distinct tandem repeating domains. One of these domains contained a 20-amino acid tandem repeating sequence enriched in threonine, serine and proline. This sequence was similar to, but not identical with, the short tandem repeating sequences identified previously in other mammalian mucins. The other domain contained a 127-amino acid tandem repeating sequence enriched in cysteine and glycine. This repeat displayed considerable sequence similarity to a family of receptor- and ligand-binding proteins containing scavenger receptor cysteine-rich repeats. By analogy with other proteins containing these cysteine-rich repeats, it is possible that, in gall-bladder mucin, this domain serves as a binding site for hydrophobic ligands such as bilirubin, cholesterol and other biliary lipids. Images Figure 4 Figure 5 Figure 6 PMID:7646470

  11. Deep Conservation of Human Protein Tandem Repeats within the Eukaryotes

    PubMed Central

    Schaper, Elke; Gascuel, Olivier; Anisimova, Maria

    2014-01-01

    Tandem repeats (TRs) are a major element of protein sequences in all domains of life. They are particularly abundant in mammals, where by conservative estimates one in three proteins contain a TR. High generation-scale duplication and deletion rates were reported for nucleic TR units. However, it is not known whether protein TR units can also be frequently lost or gained providing a source of variation for rapid adaptation of protein function, or alternatively, tend to have conserved TR unit configurations over long evolutionary times. To obtain a systematic picture, we performed a proteome-wide analysis of the mode of evolution for human protein TRs. For this purpose, we propose a novel method for the detection of orthologous TRs based on circular profile hidden Markov models. For all detected TRs, we reconstructed bispecies TR unit phylogenies across 61 eukaryotes ranging from human to yeast. Moreover, we performed additional analyses to correlate functional and structural annotations of human TRs with their mode of evolution. Surprisingly, we find that the vast majority of human TRs are ancient, with TR unit number and order preserved intact since distant speciation events. For example, ≥61% of all human TRs have been strongly conserved at least since the root of all mammals, approximately 300 Ma. Further, we find no human protein TR that shows evidence for strong recent duplications and deletions. The results are in contrast to the high generation-scale mutability of nucleic TRs. Presumably, most protein TRs fold into stable and conserved structures that are indispensable for the function of the TR-containing protein. All of our data and results are available for download from http://www.atgc-montpellier.fr/TRE. PMID:24497029

  12. Hybrid de novo tandem repeat detection using short and long reads

    PubMed Central

    2015-01-01

    Background As one of the most studied genome rearrangements, tandem repeats have a considerable impact on genetic backgrounds of inherited diseases. Many methods designed for tandem repeat detection on reference sequences obtain high quality results. However, in the case of a de novo context, where no reference sequence is available, tandem repeat detection remains a difficult problem. The short reads obtained with the second-generation sequencing methods are not long enough to span regions that contain long repeats. This length limitation was tackled by the long reads obtained with the third-generation sequencing platforms such as Pacific Biosciences technologies. Nevertheless, the gain on the read length came with a significant increase of the error rate. The main objective of nowadays studies on long reads is to handle the high error rate up to 16%. Methods In this paper we present MixTaR, the first de novo method for tandem repeat detection that combines the high-quality of short reads and the large length of long reads. Our hybrid algorithm uses the set of short reads for tandem repeat pattern detection based on a de Bruijn graph. These patterns are then validated using the long reads, and the tandem repeat sequences are constructed using local greedy assemblies. Results MixTaR is tested with both simulated and real reads from complex organisms. For a complete analysis of its robustness to errors, we use short and long reads with different error rates. The results are then analysed in terms of number of tandem repeats detected and the length of their patterns. Conclusions Our method shows high precision and sensitivity. With low false positive rates even for highly erroneous reads, MixTaR is able to detect accurate tandem repeats with pattern lengths varying within a significant interval. PMID:26399998

  13. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem r...

  14. Large-scale analysis of tandem repeat variability in the human genome

    PubMed Central

    Duitama, Jorge; Zablotskaya, Alena; Gemayel, Rita; Jansen, An; Belet, Stefanie; Vermeesch, Joris R.; Verstrepen, Kevin J.; Froyen, Guy

    2014-01-01

    Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats can alter the function and/or expression of genes allowing organisms to swiftly adapt to novel environments. Importantly, some repeat expansions have also been linked to certain neurodegenerative diseases. Therefore, accurate sequencing of tandem repeats could contribute to our understanding of common phenotypic variability and might uncover missing genetic factors in idiopathic clinical conditions. However, despite long-standing evidence for the functional role of repeats, they are largely ignored because of technical limitations in sequencing, mapping and typing. Here, we report on a novel capture technique and data filtering protocol that allowed simultaneous sequencing of thousands of tandem repeats in the human genomes of a three generation family using GS-FLX-plus Titanium technology. Our results demonstrated that up to 7.6% of tandem repeats in this family (4% in coding sequences) differ from the reference sequence, and identified a de novo variation in the family tree. The method opens new routes to look at this underappreciated type of genetic variability, including the identification of novel disease-related repeats. PMID:24682812

  15. Characterization of Tandem Repeats and Repetitive Elements in the Genomes of Mycosphaerella graminicola and M. figiensis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the genome of Mycosphaerella graminicola, the causal agent of septoria leaf blotch of wheat, a total of 22745 tandem repeat sites at least 15 bp in length were isolated for motifs from two to 250 bases long by the same processing pipeline that we have used to analyze such repeats in plant EST col...

  16. Short Tandem Repeats in Human Exons: A Target for Disease Mutations

    PubMed Central

    Madsen, Bo Eskerod; Villesen, Palle; Wiuf, Carsten

    2008-01-01

    Background In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions), are common throughout the genome, but the implications of structural variations are still not clearly understood. Long tandem repeats (e.g. microsatellites or simple repeats) are known to be hypermutable (indel-rich), but are rare in exons and only occasionally associated with diseases. Here we focus on short (imperfect) tandem repeats (STRs) which fall below the radar of conventional tandem repeat detection, and investigate whether STRs are targets for disease-related mutations in human exons. In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes. Results We show that validated human indels are extremely common in STR regions compared to non-STR regions. In contrast to longer tandem repeats, our definition of STRs found them to be present in exons of most known human genes (92%), 99% of all STR sequences in exons are shorter than 33 base pairs and 62% of all STR sequences are imperfect repeats. We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. These results are preserved when we limit the analysis to STRs outside known longer tandem repeats. Conclusion Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. In addition, STRs constitute an obvious target when screening for rare mutations, because of the relatively low amount of STRs in exons (1,973,844 bp) and the limited length of STR regions. PMID:18789129

  17. Rational design of alpha-helical tandem repeat proteins with closed architectures

    PubMed Central

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L.; Bradley, Philip

    2015-01-01

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials1,2. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks3,4. The overall architecture of tandem repeat protein structures – which is dictated by the internal geometry and local packing of the repeat building blocks – is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners5–9, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis10. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid11 repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering12–20, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that – to our knowledge – is not yet present in the protein structure database21. PMID:26675735

  18. Rational design of α-helical tandem repeat proteins with closed architectures.

    PubMed

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L; Bradley, Philip

    2015-12-24

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database. PMID:26675735

  19. Tandem repeat markers as novel diagnostic tools for high resolution fingerprinting of Wolbachia

    PubMed Central

    2012-01-01

    Background Strains of the endosymbiotic bacterium Wolbachia pipientis are extremely diverse both genotypically and in terms of their induced phenotypes in invertebrate hosts. Despite extensive molecular characterisation of Wolbachia diversity, little is known about the actual genomic diversity within or between closely related strains that group tightly on the basis of existing gene marker systems, including Multiple Locus Sequence Typing (MLST). There is an urgent need for higher resolution fingerprinting markers of Wolbachia for studies of population genetics, horizontal transmission and experimental evolution. Results The genome of the wMel Wolbachia strain that infects Drosophila melanogaster contains inter- and intragenic tandem repeats that may evolve through expansion or contraction. We identified hypervariable regions in wMel, including intergenic Variable Number Tandem Repeats (VNTRs), and genes encoding ankyrin (ANK) repeat domains. We amplified these markers from 14 related Wolbachia strains belonging to supergroup A and were successful in differentiating size polymorphic alleles. Because of their tandemly repeated structure and length polymorphism, the markers can be used in a PCR-diagnostic multilocus typing approach, analogous to the Multiple Locus VNTR Analysis (MLVA) established for many other bacteria and organisms. The isolated markers are highly specific for supergroup A and not informative for other supergroups. However, in silico analysis of completed genomes from other supergroups revealed the presence of tandem repeats that are variable and could therefore be useful for typing target strains. Conclusions Wolbachia genomes contain inter- and intragenic tandem repeats that evolve through expansion or contraction. A selection of polymorphic tandem repeats is a novel and useful PCR diagnostic extension to the existing MLST typing system of Wolbachia, as it allows rapid and inexpensive high-throughput fingerprinting of closely related strains for

  20. Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases.

    PubMed

    Feschenko, Vladimir V; Rajman, Luis A; Lovett, Susan T

    2003-02-01

    Rearrangements between tandemly repeated DNA sequences are a common source of genetic instability. Such rearrangements underlie several human genetic diseases. In many organisms, the mismatch-repair (MMR) system functions to stabilize repeats when the repeat unit is short or when sequence imperfections are present between the repeats. We show here that the action of single-stranded DNA (ssDNA) exonucleases plays an additional, important role in stabilizing tandem repeats, independent of their role in MMR. For perfect repeats of approximately 100 bp in Escherichia coli that are not susceptible to MMR, exonuclease (Exo)-I, ExoX, and RecJ exonuclease redundantly inhibit deletion. Our data suggest that >90% of potential deletion events are avoided by the combined action of these three exonucleases. Imperfect tandem repeats, less prone to rearrangements, are stabilized by both the MMR-pathway and ssDNA-specific exonucleases. For 100-bp repeats containing four mispairs, ExoI alone aborts most deletion events, even in the presence of a functional MMR system. By genetic analysis, we show that the inhibitory effect of ssDNA exonucleases on deletion formation is independent of the MutS and UvrD proteins. Exonuclease degradation of DNA displaced during the deletion process may abort slipped misalignment. Exonuclease action is therefore a significant force in genetic stabilization of many forms of repetitive DNA. PMID:12538867

  1. Child abuse in medical setting presenting as gross hematuria: diagnosis by DNA short tandem repeats.

    PubMed

    Tsai, Hsin-Lin; Yang, Ling-Yu; Chin, Tai-Wai; Chen, Po-Hon; Yen, Hsiu-Ju; Liu, Chin-Su; Wang, Hsin-Hui; Chang, Jei-Wen

    2012-07-01

    Two sisters, aged 15 and 13 years, had previous epithelioid angiomyolipoma of the kidney and suspected thin basement membrane disease, respectively. They presented with 2 years of gross hematuria and new-onset heavy proteinuria. Extensive investigations failed to find an overt cause of their urinary manifestations. The diagnosis of child abuse in a medical setting was confirmed by DNA short tandem repeats analysis, which are the first documented cases in which factitious hematuria was thus diagnosed. Complex forms of child abuse in a medical setting may require forensic tests such as DNA short tandem repeats analysis for diagnosis. PMID:22732177

  2. Broader pattern of tandem repeats in the mitochondrial control region of Perciformes

    NASA Astrophysics Data System (ADS)

    Cui, Zhaoxia; Liu, Yuan; Chu, Ka Hou

    2010-07-01

    Perciformes, the largest order of vertebrates with 20 suborders, is the most diverse fish order that dominates vertebrate ocean life. The complete mitochondrial control region (CR) of Trichiurus japonicus (Trichiuridae, Scombroidei) and Pampus sp. (Stromateidae, Stromateoidei) were amplified and sequenced. Together with data from GenBank, the tandem repeats in the mitochondrial CR from 48 species, which covered nine suborders of Perciformes, are reported in this study. The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei. The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence. Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks, which was first reported in Perciformes and vertebrates. This might have resulted from interruption of the polymerase activity during the H-strand synthesis. The four broader patterns presented here for the tandem repeats, including those in both the 5' and 3' ends, only in the either 5' or 3' end, and in the central conserved domain of the control region, will be useful for understanding the evolution of species.

  3. Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats.

    PubMed

    Brahmachary, Manisha; Guilmatre, Audrey; Quilez, Javier; Hasson, Dan; Borel, Christelle; Warburton, Peter; Sharp, Andrew J

    2014-06-01

    Tandem repeats are common in eukaryotic genomes, but due to difficulties in assaying them remain poorly studied. Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. We observed extreme variability in copy number of tandemly repeated genes, with many loci showing 5-10 fold variation in copy number among humans. Many of these loci show hallmarks of genome assembly errors, and the true copy number of many large tandem repeats is significantly under-represented even in the high quality 'finished' human reference assembly. Importantly, we demonstrate that most large tandem repeat variations are not tagged by nearby SNPs, and are therefore essentially invisible to SNP-based GWAS approaches. Using association analysis we identify many cis correlations of large tandem repeat variants with nearby gene expression and DNA methylation levels, indicating that variations of tandem repeat length are associated with functional effects on the local genomic environment. This includes an example where expansion of a macrosatellite repeat is associated with increased DNA methylation and suppression of nearby gene expression, suggesting a mechanism termed "repeat induced gene silencing", which has previously been observed only in transgenic organisms. We also observed multiple signatures consistent with altered selective pressures at tandemly repeated loci, suggesting important biological functions. Our studies show that tandemly repeated loci represent a highly variable fraction of the genome that have been systematically ignored by most previous studies, copy number variation of which can exert functionally significant effects. We suggest that future studies of tandem repeat loci will lead to many novel insights into their role in modulating

  4. A novel cell-free system reveals a mechanism of circular DNA formation from tandem repeats.

    PubMed

    Cohen, S; Mechali, M

    2001-06-15

    One characteristic of genomic plasticity is the presence of extrachromosomal circular DNA (eccDNA). High levels of eccDNA are associated with genomic instability, exposure to carcinogens and aging. We have recently reported developmentally regulated formation of eccDNA that occurs preferentially in pre-blastula Xenopus laevis embryos. Multimers of tandemly repeated sequences were over-represented in the circle population while dispersed sequences were not detected, indicating that circles were not formed at random from any chromosomal sequence. Here we present detailed mechanistic studies of eccDNA formation in a cell-free system derived from Xenopus egg extracts. We show that naked chromosomal DNA from sperm or somatic tissues serves as a substrate for direct tandem repeat circle formation. Moreover, a recombinant bacterial tandem repeat can generate eccDNA in the extract through a de novo mechanism which is independent of DNA replication. These data suggest that the presence of a high level of any direct tandem repeat can confer on DNA the ability to be converted into circular multimers in the early embryo irrespective of its sequence and that homologous recombination is involved in this process. PMID:11410662

  5. Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats.

    PubMed

    Ray, David A; Densmore, Llewellyn D

    2003-06-01

    Heteroplasmic tandem repeats in the mitochondrial control region have been documented in a wide variety of vertebrate species. We have examined the control region from 11 species in the family Crocodylidae and identified two different types of heteroplasmic repetitive sequences in the conserved sequence block (CSB) domain-an extensive poly-A tract that appears to be involved in the formation of secondary structure and a series of tandem repeats located downstream ranging from approximately 50 to approximately 80 bp in length. We describe this portion of the crocodylian control region in detail and focus on members of the family Crocodylidae. We then address the origins of the tandemly repeated sequences in this family and suggest hypotheses to explain possible mechanisms of expansion/contraction of the sequences. We have also examined control region sequences from Alligator and Caiman and offer hypotheses for the origin of tandem repeats found in those taxa. Finally, we present a brief analysis of intraindividual and interindividual haplotype variation by examining representatives of Morelet's crocodile (Crocodylus moreletii). PMID:12716979

  6. Genome-wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

    PubMed Central

    Pavlek, Martina; Gelfand, Yevgeniy; Plohl, Miroslav; Meštrović, Nevenka

    2015-01-01

    Although satellite DNAs are well-explored components of heterochromatin and centromeres, little is known about emergence, dispersal and possible impact of comparably structured tandem repeats (TRs) on the genome-wide scale. Our bioinformatics analysis of assembled Tribolium castaneum genome disclosed significant contribution of TRs in euchromatic chromosomal arms and clear predominance of satellite DNA-typical 170 bp monomers in arrays of ≥5 repeats. By applying different experimental approaches, we revealed that the nine most prominent TR families Cast1–Cast9 extracted from the assembly comprise ∼4.3% of the entire genome and reside almost exclusively in euchromatic regions. Among them, seven families that build ∼3.9% of the genome are based on ∼170 and ∼340 bp long monomers. Results of phylogenetic analyses of 2500 monomers originating from these families show high-sequence dynamics, evident by extensive exchanges between arrays on non-homologous chromosomes. In addition, our analysis shows that concerted evolution acts more efficiently on longer than on shorter arrays. Efficient genome-wide distribution of nine TR families implies the role of transposition only in expansion of the most dispersed family, and involvement of other mechanisms is anticipated. Despite similarities in sequence features, FISH experiments indicate high-level compartmentalization of centromeric and euchromatic tandem repeats. PMID:26428853

  7. Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission

    PubMed Central

    2015-01-01

    Citrus greening (huanglongbing) is the most destructive citrus disease worldwide. The disease is associated with three species of ‘Candidatus Liberibacter’ among which ‘Ca. Liberibacter asiaticus’ has the widest distribution. ‘Ca. L. asiaticus’ is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of ‘Ca. L. asiaticus’ were clearly differentiated by variable number of tandem repeat (VNTR) profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a ‘Ca. L. asiaticus’ strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of ‘Ca. L. asiaticus’ change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively. PMID:26402645

  8. Changes in Variable Number of Tandem Repeats in 'Candidatus Liberibacter asiaticus' through Insect Transmission.

    PubMed

    Katoh, Hiroshi; Inoue, Hiromitsu; Iwanami, Toru

    2015-01-01

    Citrus greening (huanglongbing) is the most destructive citrus disease worldwide. The disease is associated with three species of 'Candidatus Liberibacter' among which 'Ca. Liberibacter asiaticus' has the widest distribution. 'Ca. L. asiaticus' is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of 'Ca. L. asiaticus' were clearly differentiated by variable number of tandem repeat (VNTR) profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a 'Ca. L. asiaticus' strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of 'Ca. L. asiaticus' change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively. PMID:26402645

  9. US forensic Y-chromosome short tandem repeats database.

    PubMed

    Ge, Jianye; Budowle, Bruce; Planz, John V; Eisenberg, Arthur J; Ballantyne, Jack; Chakraborty, Ranajit

    2010-11-01

    A forensic Y-STR database generated in the US was compiled with profiles containing a portion or complete typing of 16 STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4. There were 17,447 samples in the version of database in which 77% and 20% were collected in North America and Asia, respectively. The database was separated into six general populations, African American, Asian, Caucasian, Hispanic, Indian, and Native American. Each population was further classified into subgroups according to geographic regions. Some subgroups were tested, found to be homogenous and merged together. Allele and haplotype frequencies, as well as sample sizes were summarized. Of the full haplotypes (i.e., 16 STRs without missing data), 93.7% in total population were distinct, 92.9% were population specific, and 89.3% were only observed once. The majority of shared haplotypes were found among North American populations as a result of admixture lasting the past few hundred years. The power of discrimination (PD), coancestry coefficient (F(st)), and coefficient of gene differentiation (G(st)) at locus and haplotype levels were also calculated. The most polymorphic marker was DYS385; this marker contains a tandem duplication and actually is composed of two loci. Both G(st) and F(st) estimates were very small with haplotypes composed of a high number of STRs haplotypes (e.g., 10-16 markers), although G(st) is slightly more conservative for these extended haplotypes. With Native American removed from the total population data set, the G(st) and F(st) estimates reduce further. PD was 0.9998 for the total population dataset for all 16 Y-STR markers. Three measures of Y-STR profile frequency were calculated: (1) unconditional haplotype frequency, (2) population substructure adjusted frequency, and (3) binomial upper bound of the haplotype frequency. The binomial upper bound is the most

  10. Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins.

    PubMed

    Jung, Huihun; Pena-Francesch, Abdon; Saadat, Alham; Sebastian, Aswathy; Kim, Dong Hwan; Hamilton, Reginald F; Albert, Istvan; Allen, Benjamin D; Demirel, Melik C

    2016-06-01

    Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions. Our designed sequences are based on a structural protein produced in squid suction cups that has a segmented copolymer structure with amorphous and crystalline domains. We produced segmented polypeptides with varying repeat number, while keeping the lengths and compositions of the amorphous and crystalline regions fixed. We showed that mechanical properties of these synthetic proteins could be tuned by modulating their molecular weights. Specifically, the toughness and extensibility of synthetic polypeptides increase as a function of the number of tandem repeats. This result suggests that the repetitions in native squid proteins could have a genetic advantage for increased toughness and flexibility. PMID:27222581

  11. SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure

    PubMed Central

    Landrian, Ivette; Godiska, Ronald; Shanker, Savita; Yu, Fahong; Farmerie, William G.; Ashizawa, Tetsuo

    2015-01-01

    A large, non-coding ATTCT repeat expansion causes the neurodegenerative disorder, spinocerebellar ataxia type 10 (SCA10). In a subset of SCA10 patients, interruption motifs are present at the 5’ end of the expansion and strongly correlate with epileptic seizures. Thus, interruption motifs are a predictor of the epileptic phenotype and are hypothesized to act as a phenotypic modifier in SCA10. Yet, the exact internal sequence structure of SCA10 expansions remains unknown due to limitations in current technologies for sequencing across long extended tracts of tandem nucleotide repeats. We used the third generation sequencing technology, Single Molecule Real Time (SMRT) sequencing, to obtain full-length contiguous expansion sequences, ranging from 2.5 to 4.4 kb in length, from three SCA10 patients with different clinical presentations. We obtained sequence spanning the entire length of the expansion and identified the structure of known and novel interruption motifs within the SCA10 expansion. The exact interruption patterns in expanded SCA10 alleles will allow us to further investigate the potential contributions of these interrupting sequences to the pathogenic modification leading to the epilepsy phenotype in SCA10. Our results also demonstrate that SMRT sequencing is useful for deciphering long tandem repeats that pose as “gaps” in the human genome sequence. PMID:26295943

  12. The roles of the monomer length and nucleotide context of plant tandem repeats in nucleosome positioning.

    PubMed

    Levitsky, Victor G; Babenko, Vladimir N; Vershinin, Alexander V

    2014-01-01

    Similar to regularly spaced nucleosomes in chromatin, long tandem DNA arrays are composed of regularly alternating monomers that have almost identical primary DNA structures. Such a similarity in the structural organization makes these arrays especially interesting for studying the role of intrinsic DNA preferences in nucleosome positioning. We have studied the nucleosome formation potential of DNA tandem repeat families with different monomer lengths (ML). In total, 165 plant tandem repeat families from the PlantSat database (http://w3lamc.umbr.cas.cz/PlantSat/) were divided into two classes based on the number of nucleosome repeats in one DNA monomer. For predicting nucleosome formation potential, we developed the Phase method, which combines the advantages of multiple bioinformatics models. The Phase method was able to distinguish interfamily differences and intrafamily monomer variation and identify the influence of nucleotide context on nucleosome formation potential. Three main types of nucleosome arrangement in DNA tandem repeat arrays--regular, partially regular (partial), and flexible--were distinguished among a great variety of Phase profiles. The regular type, in which all nucleosomes of the monomer array are positioned in a context-dependent manner, is the most representative type of the class 1 families, with ML equal to or a multiple of the nucleosome repeat length (NRL). In the partially regular type, nucleotide context influences the positioning of only a subset of nucleosomes. The influence of the nucleotide context on nucleosome positioning has the least effect in the flexible type, which contains the greatest number of families (65). The majority of these families belong to class 2 and have nonmultiple ML to NRL ratios. PMID:23384242

  13. A multilocus variable number tandem repeat analysis assay provides high discrimination for genotyping Leptospira santarosai strains

    PubMed Central

    Hamond, Camila; Pinna, Melissa; Medeiros, Marco Alberto; Bourhy, Pascale; Lilenbaum, Walter

    2015-01-01

    Considering the prevalence of Leptospira santarosai infections in the Americas and the scarce information about the species, we aimed to apply a multilocus variable number tandem repeat (VNTR) analysis (MLVA) for the molecular typing of L. santarosai isolates from various sources. Amplification of three VNTR loci selected from L. santarosai genome sequences resulted in a wide range of sizes for the amplified products amongst the 21 L. santarosai strains analysed. This suggested a variation in tandem repeat copy numbers in the VNTR loci. secY sequencing also showed a high nucleotide diversity, confirming the MLVA data. In conclusion, this novel MLVA provided a high level of discrimination between L. santarosai isolates, and this new typing tool could be used to investigate leptospirosis in regions where L. santarosai predominates. PMID:25721051

  14. The significance and effect of tandem repeats within the Mycobacterium tuberculosis leuA gene on alpha-isopropylmalate synthase.

    PubMed

    Chanchaem, Wimon; Palittapongarnpim, Prasit

    2008-09-01

    The 57-bp tandem repeats located in the Mycobacterium tuberculosis leuA gene code for the alpha-isopropylmalate synthase (alpha-IPMS). It is unique to this pathogen. It was previously demonstrated that the leuA-coding sequence Rv3710, containing the tandem repeats, can be translated to an active alpha-IPMS. The objective of the present study was to investigate the significance and effect of the two 57-bp tandem repeats upon gene expression and the general properties of alpha-IPMS. The putative M. tuberculosis H37Rv leuA gene with and without the tandem repeats was cloned by PCR and expressed in an Escherichia coli host. The enzyme product was studied for general properties, comparing that from a native leuA gene containing two repeats and that from the 57-bp tandem repeats deletion mutant. Upon deletion of the two 57-bp tandem repeats, the expression level of leuA from M. tuberculosis H37Rv was comparable with that of the native form. The general properties of the two types of enzymes were similar. They were both functional with the same range of optimal temperature and optimal pH for activity and with similar enzyme stability. Deletion of the repeats had no detectable effect on leuA expression level or the general properties of the enzyme product. PMID:18647358

  15. Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat.

    PubMed

    Nagaki, Kiyotaka; Tanaka, Keisuke; Yamaji, Naoki; Kobayashi, Hisato; Murata, Minoru

    2015-01-01

    The kinetochore is a protein complex including kinetochore-specific proteins that plays a role in chromatid segregation during mitosis and meiosis. The complex associates with centromeric DNA sequences that are usually species-specific. In plant species, tandem repeats including satellite DNA sequences and retrotransposons have been reported as centromeric DNA sequences. In this study on sunflowers, a cDNA-encoding centromere-specific histone H3 (CENH3) was isolated from a cDNA pool from a seedling, and an antibody was raised against a peptide synthesized from the deduced cDNA. The antibody specifically recognized the sunflower CENH3 (HaCENH3) and showed centromeric signals by immunostaining and immunohistochemical staining analysis. The antibody was also applied in chromatin immunoprecipitation (ChIP)-Seq to isolate centromeric DNA sequences and two different types of repetitive DNA sequences were identified. One was a long interspersed nuclear element (LINE)-like sequence, which showed centromere-specific signals on almost all chromosomes in sunflowers. This is the first report of a centromeric LINE sequence, suggesting possible centromere targeting ability. Another type of identified repetitive DNA was a tandem repeat sequence with a 187-bp unit that was found only on a pair of chromosomes. The HaCENH3 content of the tandem repeats was estimated to be much higher than that of the LINE, which implies centromere evolution from LINE-based centromeres to more stable tandem-repeat-based centromeres. In addition, the epigenetic status of the sunflower centromeres was investigated by immunohistochemical staining and ChIP, and it was found that centromeres were heterochromatic. PMID:26583020

  16. Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat

    PubMed Central

    Nagaki, Kiyotaka; Tanaka, Keisuke; Yamaji, Naoki; Kobayashi, Hisato; Murata, Minoru

    2015-01-01

    The kinetochore is a protein complex including kinetochore-specific proteins that plays a role in chromatid segregation during mitosis and meiosis. The complex associates with centromeric DNA sequences that are usually species-specific. In plant species, tandem repeats including satellite DNA sequences and retrotransposons have been reported as centromeric DNA sequences. In this study on sunflowers, a cDNA-encoding centromere-specific histone H3 (CENH3) was isolated from a cDNA pool from a seedling, and an antibody was raised against a peptide synthesized from the deduced cDNA. The antibody specifically recognized the sunflower CENH3 (HaCENH3) and showed centromeric signals by immunostaining and immunohistochemical staining analysis. The antibody was also applied in chromatin immunoprecipitation (ChIP)-Seq to isolate centromeric DNA sequences and two different types of repetitive DNA sequences were identified. One was a long interspersed nuclear element (LINE)-like sequence, which showed centromere-specific signals on almost all chromosomes in sunflowers. This is the first report of a centromeric LINE sequence, suggesting possible centromere targeting ability. Another type of identified repetitive DNA was a tandem repeat sequence with a 187-bp unit that was found only on a pair of chromosomes. The HaCENH3 content of the tandem repeats was estimated to be much higher than that of the LINE, which implies centromere evolution from LINE-based centromeres to more stable tandem-repeat-based centromeres. In addition, the epigenetic status of the sunflower centromeres was investigated by immunohistochemical staining and ChIP, and it was found that centromeres were heterochromatic. PMID:26583020

  17. Nonneutral evolution of tandem repeats in the mitochondrial DNA control region of lagomorphs.

    PubMed

    Casane, D; Dennebouy, N; de Rochambeau, H; Mounolou, J C; Monnerot, M

    1997-08-01

    The mitochondrial DNA of the European rabbit (Oryctolagus cuniculus) contains a tandem array of 153-bp repeats in the vicinity of the replication origin of the H-stand. Variation among molecules in the number of these repeats results in inter- and intraindividual length polymorphism (heteroplasmy). Generally, in an individual, one predominant molecular type is observed, the others representing a low percentage of the mtDNA content. At the tissue level, we observe a particular distribution of this polymorphism in the gonads compared with liver, kidneys, or brain, implying a relationship between the differentiation status of the cells and the types of new mtDNA molecules which appear and accumulate during lifetime. Similar tandem repeats were also found in the mtDNA noncoding region of European hares (Lepus europaeus), a cottontail (Sylvilagus floridanus), and a pika (Ochotona rufescens). The lengths and the sequences of these units evolve rapidly and in a concerted way, but the number of repeats is maintained in a narrow range, and an internal 20-bp segment is highly conserved. Constraints restrict the evolution of the primary sequence of these repeated units, the number of which is probably controlled by a stabilizing selection. PMID:9254915

  18. Intronic tandem repeat in the serotonin transporter gene in Old World monkeys: a new transcriptional regulator?

    PubMed

    Paredes, Ursula M; Bubb, Vivien J; Haddley, Kate; Macho, Gabriele A; Quinn, John P

    2012-06-01

    The serotonin transporter gene (SLC6A4) is heavily involved in the regulation of social behaviour of primates. Old World monkeys (e.g. macaques, baboons) have been used to study interactions between variation in the SLC6A4 gene and behaviour. Correlations of variation at one polymorphism located in the promoter region (known as 5HTTLPR) and variation at SLC6A4 expression levels, serotonin turnover and behaviour has been widely studied. In Old World monkeys, the third intron of the SLC6A4 gene also presents a tandem repeat, which sequence varies across species by a few point substitutions. We predict that in these species, this repeated region also acts as transcriptional regulatory domain and that sequence variation at this polymorphic locus might result in differential levels of expression in gene-environment interactions. For testing these hypotheses, the tandem repeat of Mandrillus sphinx and Cercopithecus aethiops from the third intron were cloned into a reporter gene vector and delivered to either primary cultures of rat neonate frontal cortex or the human cell line (JAr) to analyse their transcriptional activities. These repeated sequences supported significantly different levels of gene expression only when delivered into frontal cortex cultures. Furthermore, we tested in silico if such substitutions could have an effect on their binding profile to RNA- and DNA-binding proteins and on splicing. Taken together our results suggest that the tandem repeat in the third intron of the SLC6A4 gene of Old World monkeys could constitute a second transcriptional regulator as suggested for the 5HTTLPR and therefore contribute to diversification of serotonin-related behaviour in these primates. PMID:22038691

  19. Evolutionary analysis of the 3.3 kb tandem repeat sequence associated with facioscapulohumeral muscular dystrophy

    SciTech Connect

    Hewitt, J.E.; Clark, L.N.; Wienberg, J.

    1994-09-01

    Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant progressive disorder affecting primarily the facial and shoulder girdle muscles. The FSHD gene has been localized to distal 4q35. Genetic and physical mapping has identified a polymorphic 3.3 kb tandem repeat (D4Z4) which is closely lined to the disease. In the majority of sporadic cases there are de novo DNA rearrangements resulting in loss of an integral number of D4Z4 repeats. Sequencing of D4Z4 showed it to contain two homeoboxes and a previously identified human repeat sequences (L Sau). At present, it is not known how these rearrangements affect the pathogenesis of FSHD; however, D4Z4 clearly has an important function. It is part of a complex, dispersed human tandem repeat family which is evolutionarily conserved with a marked difference in copy number in humans and great apes compared to other species. Given the unique structure and organization of the D4Z4 repeat and its role in the FSHD disease mechanism, we have further investigated the evolutionary conservation of D4Z4. Comparison of Southern blot data from Old and New World monkeys, great apes, and humans shows that this increase in the number of D4Z4-like loci occurred after the divergence of great apes and Old World monkeys. The localization of these loci in great apes has been investigated using fluorescent in situ hybridization. These studies provide evidence that the D4Z4 repeat has evolved very recently in the great ape lineage. An understanding of how this repeat family has arisen and identification of the ancestral locus in Old World monkeys should provide clues as to the role of this sequence in FSHD.

  20. A study of allelic polymorphism of four short tandem repeats in the population of northwestern Russia

    SciTech Connect

    Aseev, M.V.; Skakun, V.N.; Baranov, V.S.

    1995-06-01

    Characteristics of the allelic polymorphisms of the trimeric AGC repeat of the androgen receptor gene (Xq11-12), exon 1 (AR); the tetrameric ATCT repeat of the von Willebrand factor gene (12p12), intron 40 (vWF); the AGAT repeat of the hypoxanthine phosphoribosyltransferase gene (Xq26) (HPRT); and the AGAT repeat of anonymous DNA sequences of the short arm of chromosome X (STRX1) were studied in 160 DNA samples from unrelated inhabitants of northwestern Russia using the method of polymerase chain reaction. Seventeen, ten, eight, and nine alleles were revealed electrophoretically for short tandem repeats of AR, vWF, HPRT, and STRX1, respectively. The heterozygosity indices for these repeats were 0.80, 0.70, 0.54, and 0.58, respectively. The values for AR and vWF correlated with those expected according to the Hardy-Weinberg equilibrium, whereas the values for HPRT and STRX1 differed significantly from those theoretically expected. The individualization potentials were 0.045, 0.135, 0.095, and 0.061 for the short tandem repeats of AR, vWF, HPRT, and STRX1, respectively. The distribution of genotypes for the set of these four loci in the population studied was determined. The possibilities of using the studied polymorphic marker systems in molecular diagnosis of the corresponding monogenic diseases - spinal and bulbar muscle atrophy (AR), Lesch-Nyhan disease (HPRT), and von Willebrand disease (vWF) - as well as in population human genetics, testing of personal identity, and molecular approaches to the estimation of mutagenic activity are discussed. 17 refs., 2 figs., 6 tabs.

  1. Variable number of tandem repeats in clinical strains of Haemophilus influenzae.

    PubMed Central

    van Belkum, A; Scherer, S; van Leeuwen, W; Willemse, D; van Alphen, L; Verbrugh, H

    1997-01-01

    An algorithm capable of identifying short repeat motifs was developed and used to screen the whole genome sequence available for Haemophilus influenzae, since some of these repeats have been shown to affect bacterial virulence. Various di- to hexanucleotide repeats were identified, confirming and extending previous findings on the existence of variable-number-of-tandem-repeat loci (VNTRs). Repeats with units of 7 or 8 nucleotides were not encountered. For all of the 3- to 6-nucleotide repeats in the H. influenzae chromosome, PCR tests capable of detecting allelic polymorphisms were designed. Fourteen of 18 of the potential VNTRs were indeed highly polymorphic when different strains were screened. Two of the potential VNTRs appeared to be short and homogeneous in length; another one may be specific for the H. influenzae Rd strain only. One of the primer sets generated fingerprint-type DNA banding patterns. The various repeat types differed with respect to intrinsic stability as well. It was noted for separate colonies derived from a single clinical specimen or strains passaged for several weeks on chocolate agar plates that the lengths of the VNTRs did not change. When several strains from different patients infected during an outbreak of lung disease were analyzed, increased but limited variation was encountered in all VNTR sites analyzed. One of the 5-nucleotide VNTRs proved to be hypervariable. This variability may reflect the molecular basis of a mechanism used by H. influenzae bacteria to successfully colonize and infect different human individuals. PMID:9393791

  2. The tandem-repeat polymorphism of the DC-SIGNR gene in HCV infection.

    PubMed

    Nattermann, J; Ahlenstiel, G; Berg, T; Feldmann, G; Nischalke, H D; Müller, T; Rockstroh, J; Woitas, R; Sauerbruch, T; Spengler, U

    2006-01-01

    The C-type lectin DC-SIGNR has been shown to bind hepatitis C virus (HCV). Here, we analysed the tandem-repeat polymorphism of the DC-SIGNR gene with respect to intraindividual HCV replication. In a cross-sectional comparison HCV-infected patients (n = 430) and healthy subjects (n = 100) were genotyped for the DC-SIGNR polymorphism using PCR. The distribution of DC-SIGNR alleles did not differ significantly between the two groups. However, HCV-infected patients with 5-, 6-, and 7-repeat alleles had higher HCV-RNA levels when compared with carriers of 4- and 9-repeat alleles (P < 0.05). Thus, the DC-SIGNR polymorphism might affect HCV loads supporting the concept that DC-SIGNR contributes to HCV replication efficacy. PMID:16364081

  3. Effects of Short-term Exposure to Inhalable Particulate Matter on DNA Methylation of Tandem Repeats

    PubMed Central

    Guo, Liqiong; Byun, Hyang-Min; Zhong, Jia; Motta, Valeria; Barupal, Jitendra; Zheng, Yinan; Dou, Chang; Zhang, Feiruo; McCracken, John P.; Diaz, Anaité; Marco, Sanchez-Guerra; Colicino, Silvia; Schwartz, Joel; Wang, Sheng; Hou, Lifang; Baccarelli, Andrea A.

    2015-01-01

    There is compelling evidence that particulate matter (PM) increases lung cancer risk by triggering systemic inflammation, and leukocyte DNA hypomethylation. However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. Tandem repeats, which display a greater propensity to mutate, and are often hypomethylated in cancer patients, have never been investigated in individuals exposed to PM. We measured methylation of three tandem repeats (SATα, NBL2, D4Z4) by polymerase chain reaction–pyrosequencing on blood samples from truck drivers and office workers (60 per group) in Beijing, China. We used lightweight monitors to measure personal PM2.5 (PM with aerodynamic diameter ≤2.5 µm) and elemental carbon (EC, a tracer of PM from vehicular traffic). Ambient PM10 data were obtained from air quality measuring stations. Overall, an interquartile increase in personal PM2.5 and ambient PM10 levels was associated with a significant covariate-adjusted decrease in SATα methylation (−1.35% 5-methyl cytosine [5mC], P = 0.01; and −1.33%5mC; P = 0.01, respectively). Effects from personal PM2.5 and ambient PM10 on SATα methylation were stronger in truck drivers (−2.34%5mC, P = 0.02; −1.44%5mC, P = 0.06) than office workers (−0.95%5mC, P = 0.26; −1.25%5mC, P = 0.12, respectively). Ambient PM10 was negatively correlated with NBL2 methylation in truck drivers (−1.38%5mC, P = 0.03) but not in office workers (1.04%5mC, P = 0.13). Our result suggests that PM exposure is associated with hypomethylation of selected tandem repeats. Measuring tandem-repeat hypomethylation in easy-to-obtain blood specimens might identify individuals with biological effects and potential cancer risk from PM exposure. PMID:24436168

  4. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing.

    PubMed

    Warshauer, David H; Churchill, Jennifer D; Novroski, Nicole; King, Jonathan L; Budowle, Bruce

    2015-08-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles. PMID:26391384

  5. Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats.

    PubMed Central

    Stupar, Robert M; Song, Junqi; Tek, Ahmet L; Cheng, Zhukuan; Dong, Fenggao; Jiang, Jiming

    2002-01-01

    The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S.25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats. PMID:12454086

  6. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    PubMed Central

    Warshauer, David H.; Churchill, Jennifer D.; Novroski, Nicole; King, Jonathan L.; Budowle, Bruce

    2015-01-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles. PMID:26391384

  7. Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome.

    PubMed

    Klevytska, A M; Price, L B; Schupp, J M; Worsham, P L; Wong, J; Keim, P

    2001-09-01

    Yersinia pestis, the infamous plague-causing pathogen, appears to have emerged in relatively recent history. Evidence of this fact comes from several studies that document a lack of nucleotide diversity in the Y. pestis genome. In contrast, we report that variable-number tandem repeat (VNTR) sequences are common in the Y. pestis genome and occur frequently in gene coding regions. Larger tandem repeat arrays, most useful for phylogenetic analysis, are present at an average of 2.18 arrays per 10 kbp and are distributed evenly throughout the genome and the two virulence plasmids, pCD1 and pMT1. We examined allelic diversity at 42 chromosomal VNTR loci in 24 selected isolates (12 globally distributed and 12 from Siskiyou County, Calif.). Vast differences in diversity were observed among the 42 VNTR loci, ranging from 2 to 11 alleles. We found that the maximum copy number of repeats in an array was highly correlated with diversity (R = 0.86). VNTR-based phylogenetic analysis of the 24 strains successfully grouped isolates from biovar orientalis and most of the antiqua and mediaevalis strains. Hence, multiple-locus VNTR analysis (MLVA) appears capable of both distinguishing closely related strains and successfully classifying more distant relationships. Harnessing the power of MLVA to establish standardized databases will enable researchers to better understand plague ecology and evolution around the world. PMID:11526147

  8. Abundant contribution of short tandem repeats to gene expression variation in humans

    PubMed Central

    Gymrek, Melissa; Willems, Thomas; Guilmatre, Audrey; Zeng, Haoyang; Markus, Barak; Georgiev, Stoyan; Daly, Mark J.; Price, Alkes L.; Pritchard, Jonathan; Sharp, Andrew

    2016-01-01

    The contribution of repetitive elements to quantitative human traits is largely unknown. Here, we report a genome-wide survey of the contribution of Short Tandem Repeats (STRs), one of the most polymorphic and abundant repeat classes, to gene expression in humans. Our survey identified 2,060 significant expression STRs (eSTRs). These eSTRs were replicable in orthogonal populations and expression assays. We used variance partitioning to disentangle the contribution of eSTRs from linked SNPs and indels and found that eSTRs contribute 10%–15% of the cis-heritability mediated by all common variants. Further functional genomic analyses showed that eSTRs are enriched in conserved regions, co-localize with regulatory elements, and can modulate certain histone modifications. By analyzing known GWAS hits and searching for new associations in 1,685 deeply-phenotyped whole-genomes, we found that eSTRs are enriched in various clinically-relevant conditions. These results highlight the contribution of short tandem repeats to the genetic architecture of quantitative human traits. PMID:26642241

  9. Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.

    PubMed

    Anisimova, Maria; Pečerska, Julija; Schaper, Elke

    2015-01-01

    Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions and can be associated with virulence, resistance, and infectious/neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this review, we discuss these intricacies and their consequences. We present our recent contributions to computational and statistical approaches for TR significance testing, sequence profile-based TR annotation, TR-aware sequence alignment, phylogenetic analyses of TR unit number and order, and TR benchmarks. Importantly, all these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features. PMID:25853125

  10. Cloning of a cuticular antigen that contains multiple tandem repeats from the filarial parasite Dirofilaria immitis.

    PubMed Central

    Poole, C B; Grandea, A G; Maina, C V; Jenkins, R E; Selkirk, M E; McReynolds, L A

    1992-01-01

    An unusual antigen composed of tandemly repeated protein units was cloned from the filarial parasite Dirofilaria immitis. The antigen was initially identified by screening a lambda gt11 cDNA library with serum from dogs immunized with irradiated D. immitis third-stage larvae. DNA sequence analysis of the cDNA clone, Di5, revealed a continuous open reading frame composed of two 399-base-pair repeats arranged in tandem. Southern blot analysis of genomic D. immitis DNA showed that the gene coding for Di5 is composed of a tandem array of 25-50 copies of this same 399-base-pair repeat. Antiserum raised against recombinant Di5 protein detected a protein "ladder," from about 14 to greater than 200 kDa with steps approximately 15 kDa apart, on immunoblots of D. immitis extract. Metabolic labeling of adult parasites with [35S]methionine showed that Di5 is synthesized as a large precursor that is subsequently cleaved to produce the ladder-like array. These results suggest that the characteristic ladder is created by proteolytic cleavage of the precursor at the same site in each monomer. The Di5 antigen was localized to the cuticle and hypodermis of adult D. immitis by immunoelectron microscopy. Both male and female parasites were found to release Di5 when cultured in vitro. DNA hybridization analysis demonstrated that Di5 is a member of a gene family present in many filarial parasites that infect both animal and human populations. Images PMID:1631084

  11. Altered Methylation in Tandem Repeat Element and Elemental Component Levels in Inhalable Air Particles

    PubMed Central

    Hou, Lifang; Zhang, Xiao; Zheng, Yinan; Wang, Sheng; Dou, Chang; Guo, Liqiong; Byun, Hyang-Min; Motta, Valeria; McCracken, John; Díaz, Anaité; Kang, Choong-Min; Koutrakis, Petros; Bertazzi, Pier Alberto; Li, Jingyun; Schwartz, Joel; Baccarelli, Andrea A.

    2014-01-01

    Exposure to particulate matter (PM) has been associated with lung cancer risk in epidemiology investigations. Elemental components of PM have been suggested to have critical roles in PM toxicity, but the molecular mechanisms underlying their association with cancer risks remain poorly understood. DNA methylation has emerged as a promising biomarker for environmental-related diseases, including lung cancer. In this study, we evaluated the effects of PM elemental components on methylation of three tandem repeats in a highly-exposed population in Beijing, China. The Beijing Truck Driver Air Pollution Study was conducted shortly before the 2008 Beijing Olympic Games (June 15-July 27, 2008) and included 60 truck drivers and 60 office workers. On two days separated by 1-2 weeks, we measured blood DNA methylation of SATα, NBL2, D4Z4, and personal exposure to eight elemental components in PM2.5, including aluminum (Al), silicon (Si), sulfur (S), potassium (K), calcium (Ca) titanium (Ti), iron (Fe), and zinc (Zn). We estimated the associations of individual elemental component with each tandem repeat methylation in generalized estimating equations (GEE) models adjusted for PM2.5 mass and other covariates. Out of the eight examined elements, NBL2 methylation was positively associated with concentrations of Si (0.121, 95%CI: 0.030; 0.212, FDR=0.047) and Ca (0.065, 95%CI: 0.014; 0.115, FDR=0.047) in truck drivers. In office workers, SATα methylation was positively associated with concentrations of S (0.115, 95%CI: 0.034; 0.196, FDR=0.042). PM-associated differences in blood tandem-repeat methylation may help detect biological effects of the exposure and identify individuals who may eventually experience higher lung cancer risk. PMID:24273195

  12. STaRRRT: a table of short tandem repeats in regulatory regions of the human genome

    PubMed Central

    2013-01-01

    Background Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. In humans, polymorphic TRs are known to cause neurodegenerative and neuromuscular disorders as well as being associated with complex diseases such as diabetes and cancer. If present in upstream regulatory regions, TRs can modify chromatin structure and affect transcription; resulting in altered gene expression and protein abundance. The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are considerably more polymorphic than coding region STRs. As such, they may be a common driver of phenotypic variation. To study STRs located in regulatory regions, we have performed genome-wide analysis to identify all STRs present in a region that is 2 kilobases upstream and 1 kilobase downstream of the transcription start sites of genes. Results The Short Tandem Repeats in Regulatory Regions Table, STaRRRT, contains the results of the genome-wide analysis, outlining the characteristics of 5,264 STRs present in the upstream regulatory region of 4,441 human genes. Gene set enrichment analysis has revealed significant enrichment for STRs in cellular, transcriptional and neurological system gene promoters and genes important in ion and calcium homeostasis. The set of enriched terms has broad similarity to that seen in coding regions, suggesting that regulatory region STRs are subject to similar evolutionary pressures as STRs in coding regions and may, like coding region STRs, have an important role in controlling gene expression. Conclusions STaRRRT is a readily-searchable resource for investigating potentially polymorphic STRs that could influence the expression of any gene of interest. The processes and genes enriched for regulatory region STRs provide potential novel targets for diagnosing and treating disease, and support a role for these STRs in the evolution of the human genome. PMID:24228761

  13. Recurrent simple tandem repeat mutations during human Y-chromosome radiation in Caucasian subpopulations.

    PubMed

    Ciminelli, B M; Pompei, F; Malaspina, P; Hammer, M; Persichetti, F; Pignatti, P F; Palena, A; Anagnou, N; Guanti, G; Jodice, C

    1995-12-01

    The haplotypes at four polymorphic loci of the Y chromosome were determined in 245 Caucasian males from 12 subpopulations. The data show that haplotype radiation occurred among Caucasians. Haplotype radiation was accompanied by recurrent mutations at STR loci that caused partial randomization of haplotype structure. The present distribution of alleles at short tandem repeats (STRs) can be explained by a mutation pattern similar to those described for autosomal STRs. The degree of variation among groups of subpopulations was assayed by using the Analysis of Molecular Variance. The results confirm a faster divergence of the Y chromosome as compared to the rest of the genome. PMID:8587142

  14. A region of euchromatin coincides with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome.

    PubMed

    Darrow, Emily M; Seberg, Andrew P; Das, Sunny; Figueroa, Debbie M; Sun, Zhuo; Moseley, Shawn C; Chadwick, Brian P

    2014-09-01

    Euchromatic features are largely absent from the human inactive X chromosome (Xi), with the exception of several large tandem repeats that can be detected as euchromatin bands at metaphase. Despite residing megabases apart, these tandem repeats make frequent inactive X-specific interactions. The mouse homologue has been reported for at least one of the tandem repeats, but whether the mouse Xi is also characterized by distinct bands of euchromatin remains unknown. We examined the mouse Xi for the presence of euchromatin bands by examining the pattern of histone H3 dimethylated at lysine 4 and detected two major signals. The first band resides in the subtelomeric region of band XF5 and may correspond to the pseudoautosomal region. The second band localizes to XE3 and coincides with an extensive complex repeat composed of a large tandem and inverted repeat segment as well as several large short interspersed nuclear element (SINE)-rich tandem repeats. Fluorescence in situ hybridization reveals that sequences with homology to the repeat region are scattered along the length of the Y chromosome. Immunofluorescence analysis of histone H3 trimethylated at lysine 9 on metaphase chromosomes indicates that the repeat region corresponds to a band of constitutive heterochromatin on the male X and female active X chromosomes, whereas the euchromatin signal appears to be female specific. These data suggest that the band of euchromatin observed at XE3 is unique to the mouse Xi, comparable to the chromatin arrangement of several large tandem repeats located on the human X chromosome. PMID:24821208

  15. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence.

    PubMed

    Bilgin Sonay, Tugce; Carvalho, Tiago; Robinson, Mark D; Greminger, Maja P; Krützen, Michael; Comas, David; Highnam, Gareth; Mittelman, David; Sharp, Andrew; Marques-Bonet, Tomàs; Wagner, Andreas

    2015-11-01

    Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1-5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2-50 bp). Genes that contained TRs in the promoters, in their 3' untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1-5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation. PMID:26290536

  16. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

    PubMed Central

    Bilgin Sonay, Tugce; Carvalho, Tiago; Robinson, Mark D.; Greminger, Maja P.; Krützen, Michael; Comas, David; Highnam, Gareth; Mittelman, David; Sharp, Andrew; Marques-Bonet, Tomàs; Wagner, Andreas

    2015-01-01

    Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1–5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2–50 bp). Genes that contained TRs in the promoters, in their 3′ untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1–5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation. PMID:26290536

  17. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

    PubMed Central

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E.; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D.

    2015-01-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. PMID:25823460

  18. Bovine submaxillary mucin contains multiple domains and tandemly repeated non-identical sequences.

    PubMed Central

    Jiang, W; Woitach, J T; Keil, R L; Bhavanandan, V P

    1998-01-01

    A number of cDNA fragments coding for bovine submaxillary mucin (BSM) were cloned, and the nucleotide sequence of the largest clone, BSM421, was determined. Two peptide sequences determined from the purified apoBSM were found near the N-terminus of the mucin-coding region of BSM421. This clone does not contain a start or stop codon, but its 3' end overlaps with the 5' end of a previously isolated clone, lambdaBSM10. The composite sequence of 1589 amino acid residues consists of five distinct protein domains, which are numbered from the C-terminus. The cysteine-rich domain I can be further divided into a von Willebrand factor type C repeat and a cystine knot. Domains III and V consist of similar repeated peptide sequences with an average of 47 residues. Domains II and IV do not contain such sequences but are similar to domains III and V in being rich in serine and threonine, many of which are predicted to be potential O-glycosylation sites. Domain III also contains two sequences that match the ATP/GTP-binding site motif A (P-loop). Only beta-strands and no alpha-helices are predicted for the partial deduced amino acid sequence. Northern analysis of submaxillary gland RNA with the BSM421 probe detected multiple messages of BSM with sizes from 1.1 to over 10 kb. The tandemly repeated, non-identical peptide sequences of approx. 47 residues in domains III and V of BSM differ from the tandemly repeated, identical 81-residue sequences of pig submaxillary mucin (PSM), although both BSM and PSM contain similar C-terminal domains. In contrast, two peptide sequences of ovine submaxillary mucin are highly similar (86% and 65% identical respectively) to the corresponding sequences in domain V of BSM. PMID:9512479

  19. Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua.

    PubMed

    Arnason, E; Rand, D M

    1992-09-01

    The mitochondrial DNA of the Atlantic cod (Gadus morhua) contains a tandem array of 40-bp repeats in the D-loop region of the molecule. Variation among molecules in the copy number of these repeats results in mtDNA length variation and heteroplasmy (the presence of more than one form of mtDNA in an individual). In a sample of fish collected from different localities around Iceland and off George's Bank, each individual was heteroplasmic for two or more mtDNAs ranging in repeat copy number from two (common) to six (rare). An earlier report on mtDNA heteroplasmy in sturgeon (Acipenser transmontanus) presented a competitive displacement model for length mutations in mtDNAs containing tandem arrays and the cod data deviate from this model. Depending on the nature of putative secondary structures and the location of D-loop strand termination, additional mechanisms of length mutation may be needed to explain the range of mtDNA length variants maintained in these populations. The balance between genetic drift and mutation in maintaining this length polymorphism is estimated through a hierarchical analysis of diversity of mtDNA length variation in the Iceland samples. Eighty percent of the diversity lies within individuals, 8% among individuals and 12% among localities. An estimate of theta = 2N(eo) mu greater than 1 indicates that this system is characterized by a high mutation rate and is governed primarily by deterministic dynamics. The sequences of repeat arrays from fish collected in Norway, Iceland and George's Bank show no nucleotide variation suggesting that there is very little substructuring to the North Atlantic cod population. PMID:1356884

  20. Characterization of Leptospira interrogans Serovars by Polymorphism Variable Number Tandem Repeat Analysis

    PubMed Central

    Rezasoltani, Sama; Dabiri, Hossein; Khaki, Pejvak; Rostami Nejad, Mohammad; Karimnasab, Nasim; Modirrousta, Shiva

    2015-01-01

    Background: Leptospirosis is recognized as a re-emerging infectious disease; therefore, understanding the epidemiology of the disease is vital for designing intervention programs and diminishing its transmission. Recently, Multilocus variable number tandem repeat analysis (MLVA) is used for segregating and identifying Leptospira serovars. The method has potential application in investigating the molecular epidemiology of Leptospira. Objectives: The propose of this study was genomic identification of pathogenic Leptospires in Iran by MLVA. Materials and Methods: Leptospira serovars were obtained from National Reference Laboratory of Leptospira at Razi Vaccine and Serum Research Institute, Karaj, Iran. Serovars were cultured into the liquid EMJH medium and incubated at 28˚C for 7 days. DNA of serovars was extracted using the phenol-chloroform method. PCR was performed with 5 selected variable number tandem repeat analysis (VNTR) loci. The amplified products were analyzed by agarose gel electrophoresis. The size of the amplified products was estimated by 100 bp ladder and sequencing analysis. Results: The saprophytic serovar showed no amplified fragments. PCR products in all pathogenic serovars were observed. The 12 reference serovars used for the development of technique displayed distinct patterns. Conclusions: Results showed that MLVA technique with its range of polymorphism is a good marker for identification of pathogenic serovars. Some VNTR loci are more powerful than the other ones with regard to differentiation. Serovars from the same geographical area have more genetic similarity than same serovars from different places. MLVA is a suitable technique for epidemiological survey. PMID:26568805

  1. Tandem repeated application of organic solvents and sodium lauryl sulphate enhances cumulative skin irritation.

    PubMed

    Schliemann, Sibylle; Schmidt, Christina; Elsner, Peter

    2014-01-01

    The objective of our study was to investigate the tandem irritation potential of two organic solvents with concurrent exposure to the hydrophilic detergent irritant sodium lauryl sulphate (SLS). A tandem repeated irritation test was performed with two undiluted organic solvents, cumene (C) and octane (O), with either alternating application with SLS 0.5% or twice daily application of each irritant alone in 27 volunteers on the skin of the back. The cumulative irritation induced over 4 days was quantified using visual scoring and non-invasive bioengineering measurements (skin colour reflectance, skin hydration and transepidermal water loss). Repeated application of C/SLS and O/SLS induced more decline of stratum corneum hydration and higher degrees of clinical irritation and erythema compared to each irritant alone. Our results demonstrate a further example of additive harmful skin effects induced by particular skin irritants and indicate that exposure to organic solvents together with detergents may increase the risk of acquiring occupational contact dermatitis. PMID:24457469

  2. Multiple-locus variable-number tandem repeat analysis for strain typing of Clostridium perfringens.

    PubMed

    Sawires, Youhanna S; Songer, J Glenn

    2005-10-01

    Clostridium perfringens is ubiquitous in the environment and causes diseases in man and animals, with syndromes ranging from enteritis, enterotoxemia, and sudden death to food poisoning and gas gangrene. Understanding the epidemiology of these infections and of the evolution of virulence in C. perfringens necessitate an efficient, time and cost effective strain typing method. Multiple-locus variable-number tandem repeat analysis (MLVA) has been applied to typing of other pathogens and we describe here the development of a MLVA scheme for C. perfringens. We characterized five variable tandem repeat (VNTR) loci, four of which are contained within protein encoding genes and screened 112 C. perfringens isolates to evaluate typability, reproducibility, and discriminatory power of the scheme. All the isolates were assigned a MLVA genotype and the technique has excellent reproducibility, with a numerical index of discrimination for the five VNTR loci of 0.995. Thus MLVA is an efficient tool for C. perfringens strain typing, and being PCR based makes it rapid, easy, and cost effective. In addition, it can be employed in epidemiological, ecological, and evolutionary investigations of the organism. PMID:16701582

  3. Amyloid formation and disaggregation of {alpha}-synuclein and its tandem repeat ({alpha}-TR)

    SciTech Connect

    Bae, Song Yi; Kim, Seulgi; Hwang, Heejin; Kim, Hyun-Kyung; Yoon, Hyun C.; Kim, Jae Ho; Lee, SangYoon; Kim, T. Doohun

    2010-10-01

    Research highlights: {yields} Formation of the {alpha}-synuclein amyloid fibrils by [BIMbF{sub 3}Im]. {yields} Disaggregation of amyloid fibrils by epigallocatechin gallate (EGCG) and baicalein. {yields} Amyloid formation of {alpha}-synuclein tandem repeat ({alpha}-TR). -- Abstract: The aggregation of {alpha}-synuclein is clearly related to the pathogenesis of Parkinson's disease. Therefore, detailed understanding of the mechanism of fibril formation is highly valuable for the development of clinical treatment and also of the diagnostic tools. Here, we have investigated the interaction of {alpha}-synuclein with ionic liquids by using several biochemical techniques including Thioflavin T assays and transmission electron microscopy (TEM). Our data shows a rapid formation of {alpha}-synuclein amyloid fibrils was stimulated by 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [BIMbF{sub 3}Im], and these fibrils could be disaggregated by polyphenols such as epigallocatechin gallate (EGCG) and baicalein. Furthermore, the effect of [BIMbF{sub 3}Im] on the {alpha}-synuclein tandem repeat ({alpha}-TR) in the aggregation process was studied.

  4. Multiplex variable number of tandem repeats for Oenococcus oeni and applications.

    PubMed

    Claisse, Olivier; Lonvaud-Funel, Aline

    2014-04-01

    Oenococcus oeni is responsible for the malolactic fermentation of wine. Genomic diversity has already been established in this species. In addition, winemakers usually report varying starter-culture efficiency. It is essential to monitor indigenous and selected strains in order to understand strain survival and development during the winemaking process. A previous article described a variable number of tandem repeats (VNTR) scheme, based on five polymorphic loci of the genome. VNTR typing of O. oeni was highly discriminating, faster, and more reliable than the PFGE or MLST methods. The objective of this study was to set up a faster protocol by multiplexing, taking advantage of the high performance of multicolor capillary electrophoresis. The primers were labeled with multiple fluorescent dyes. PCR conditions were adapted by multiplexing amplifications in two separate PCR mixtures for the five loci, both at the same annealing temperature. The resulting assay proved to be robust, accurate, fast and easy to perform. Thanks to this new protocol, all O. oeni strains used in the study were typed using the five tandem repeats (TR). As expected, the primers for the five TR loci were specific to O. oeni. The method was improved to analyze isolated and mixed colonies, as well as bacteria harvested from wine using fast technology for analysis of nucleic acids (FTA(®)) technology. Finally, predictive models were constructed, to predict phylogenetic relationships and associate bacterial strain resistance to freeze-drying with fragment length analysis (FLA) profiles and genotypic and phenotypic characters. PMID:24290630

  5. Highly repeated DNA sequences in birds: the structure and evolution of an abundant, tandemly repeated 190-bp DNA fragment in parrots.

    PubMed

    Madsen, C S; de Kloet, D H; Brooks, J E; de Kloet, S R

    1992-10-01

    Up to 6.8% of the parrot (Psittaciformes) genome consists of a tandemly repeated, 190-bp sequence (P1) located in the centromere of many if not all chromosomes. Monomer repeats from 10 different psittacine species representing four subfamilies were isolated and cloned. The intraspecific sequence variation ranged from 1.5 to 7%. The interspecific sequence variation ranged from less than 3% between two species of cockatoos to approximately 45% between cockatoos and other parrots. The monomer sequences of all 10 parrot species contained several conserved (> 90%) sequence elements at identical locations within the repeat. A comparison with tandemly repeated DNA sequences in other avian species showed that several of these conserved elements were also present at similar locations within the 184-bp repeat of the Chilean flamingo (Phoenicopterus chilensis), suggesting a great antiquity of the repeat. One of the elements was also found in the tandemly repeated sequences of the crane (Gruidae) and falcon (Falconidae) families. The data were used for the construction of a partial most parsimonious relationship that supports a regional subdivision of the Psittaciformes. PMID:1339392

  6. Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae)

    PubMed Central

    Wang, Xiaoyang; Liu, Nian; Zhang, Hongli; Yang, Xiao-Jun; Huang, Yuan; Lei, Fumin

    2015-01-01

    To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5′ imperfect copy at its downstream and a 3′ imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3′ and 5′ imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure. PMID:26288099

  7. Variation of intragenic tandem repeat tract of tolA modulates Escherichia coli stress tolerance.

    PubMed

    Zhou, Kai; Michiels, Chris W; Aertsen, Abram

    2012-01-01

    In recent work we discovered that the intragenic tandem repeat (TR) region of the tolA gene is highly variable among different Escherichia coli strains. The aim of this study was therefore to investigate the biological function and dynamics of TR variation in E. coli tolA. The biological impact of TR variation was examined by comparing the ability of a set of synthetic tolA variants with in frame repeat copies varying from 2 to 39 to rescue the altered susceptibility of an E. coli ΔtolA mutant to deoxycholic acid, sodium dodecyl sulfate, hyperosmolarity, and infection with filamentous bacteriophage. Interestingly, although each of the TolA variants was able to at least partly rescue the ΔtolA mutant, the extent was clearly dependent on both the repeat number and the type of stress imposed, indicating the existence of opposing selective forces with regard to the optimal TR copy number. Subsequently, TR dynamics in a clonal population were assayed, and we could demonstrate that TR contractions are RecA dependent and enhanced in a DNA repair deficient uvrD background, and can occur at a frequency of 6.9×10(-5). PMID:23094082

  8. Genome-wide identification of human- and primate-specific core promoter short tandem repeats.

    PubMed

    Bushehri, A; Barez, M R Mashhoudi; Mansouri, S K; Biglarian, A; Ohadi, M

    2016-08-01

    Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation. PMID:27108803

  9. TAPO: A combined method for the identification of tandem repeats in protein structures.

    PubMed

    Do Viet, Phuong; Roche, Daniel B; Kajava, Andrey V

    2015-09-14

    In recent years, there has been an emergence of new 3D structures of proteins containing tandem repeats (TRs), as a result of improved expression and crystallization strategies. Databases focused on structure classifications (PDB, SCOP, CATH) do not provide an easy solution for selection of these structures from PDB. Several approaches have been developed, but no best approach exists to identify the whole range of 3D TRs. Here we describe the TAndem PrOtein detector (TAPO) that uses periodicities of atomic coordinates and other types of structural representation, including strings generated by conformational alphabets, residue contact maps, and arrangements of vectors of secondary structure elements. The benchmarking shows the superior performance of TAPO over the existing programs. In accordance with our analysis of PDB using TAPO, 19% of proteins contain 3D TRs. This analysis allowed us to identify new families of 3D TRs, suggesting that TAPO can be used to regularly update the collection and classification of existing repetitive structures. PMID:26320412

  10. Evaluation of 13 short tandem repeated loci for use in personal identification applications

    SciTech Connect

    Hammond, H.A.; Caskey, C.T. ); Jin, L.; Zhong, Y.; Chakraborty, R. )

    1994-07-01

    Personal identification by using DNA typing methodologies has been an issue in the popular and scientific press for several years. The authors present a PCR-based DNA-typing method using 13 unlinked short tandem repeat (STR) loci. Validation of the loci and methodology has been performed to meet standards set by the forensic community and the accrediting organization for parentage testing. Extensive statistical analysis has addressed the issues surrounding the presentation of [open quotes]match[close quotes] statistics. The authors have found STR loci to provide a rapid, sensitive, and reliable method of DNA typing for parentage testing, forensic identification, and medical diagnostics. Valid statistical analysis is generally simpler than similar analysis of RFLP-VNTR results and provides powerful statistical evidence of the low frequency of random multilocus genotype matching. 54 refs., 4 figs., 6 tabs.

  11. The discovery, function and development of the variable number tandem repeats in different Mycobacterium species.

    PubMed

    Sun, Zhaogang; Li, Weimin; Xu, Shaofa; Huang, Hairong

    2016-09-01

    The method of genotyping by variable number tandem repeats (VNTRs) facilitates the epidemiological studies of different Mycobacterium species worldwide. Until now, the VNTR method is not fully understood, for example, its discovery, function and classification. The inconsistent nomenclature and terminology of VNTR is especially confusing. In this review, we first describe in detail the VNTRs in Mycobacterium tuberculosis (M. tuberculosis), as this pathogen resulted in more deaths than any other microbial pathogen as well as for which extensive studies of VNTRs were carried out, and then we outline the recent progress of the VNTR-related epidemiological research in several other Mycobacterium species, such as M. abscessus, M. africanum, M. avium, M. bovis, M. canettii, M. caprae, M. intracellulare, M. leprae, M. marinum, M. microti, M. pinnipedii and M. ulcerans from different countries and regions. This article is aimed mainly at the practical notes of VNTR to help the scientists in better understanding and performing this method. PMID:26089025

  12. Establishing the robustness of short-tandem-repeat statistics for forensic applications.

    PubMed Central

    Evett, I. W.; Gill, P. D.; Scrange, J. K.; Weir, B. S.

    1996-01-01

    Before the introduction of a four-locus multiplex short-tandem-repeat (STR) system into casework, an extensive series of tests were carried out to determine robust procedures for assessing the evidential value of a match between crime and suspect samples. Twelve databases were analyzed from the three main ethnic groups encountered in casework in the United Kingdom: Caucasians, Afro-Caribbeans, and Asians from the Indian subcontinent. Independence tests resulted in a number of significant results, and the impact that these might have on forensic casework was investigated. It is demonstrated that previously published methods provide a simple procedure for correcting allele frequencies--and that this leads to conservative casework estimates of evidential value. PMID:8571967

  13. [Detection of short tandem repeat (STR) polymorphisms by microchip electrophoresis for individual identification of cattle].

    PubMed

    Yamaguchi, Akihiro; Shimizu, Kaori; Mishima, Takashi; Hattori, Hideki; Katsuda, Shin-ichi; Sato, Hidetaka; Ueda, Nobuo; Sato, Noriyuki

    2006-12-01

    A simple and rapid detection of short tandem repeat (STR) markers was studied as a screening test for individual identification of cattle. DNAs were extracted from eight commercial beef samples by a proteinase K-boil method followed by purification with 2-propanol precipitation. Five STR markers, known to be highly polymorphic, were amplified by PCR and analyzed both by a conventional sequencing analysis (SEQ) and by a proposed microchip electrophoresis (MEP). Every marker revealed high polymorphism, such as 5-9 alleles in SEQ analysis, and 4-6 alleles in MEP analysis. This simple and rapid MEP analysis is expected to be an effective screening tool with use of confirmatory SEQ analysis. PMID:17228791

  14. Mutations of short tandem repeat loci in cases of paternity testing in Chinese.

    PubMed

    Sun, Mao; Zhang, XiaoNan; Wu, Dan; Shen, Qi; Wu, YuanMing; Fu, ShanMin

    2016-09-01

    In order to find out the characteristics of genetic mutations in 15 short tandem repeat (STR) loci, 3734 parentage cases were analyzed using AmpFlSTR Sinofiler kit. The allele source, mutation rate, and mutation rule of the STR loci were determined. Seventy mutations were observed in all cases for paternity testing. Among 15 STR loci, the highest mutation rate was observed in D12S391 (0.21 %), but the D5S818 gene mutation rate was relatively low (0.02 %). One-step mutation cases accounted for 95.7 % of all of the cases monitored. And the mutations in this study mainly showed paternal mutation (64/70). The research results are of great significance for identification and paternity tests and for the improvement of genetic studies on Chinese population in the future. PMID:26223683

  15. Short tandem repeat (STR) locus HUMD8S306 in a large population sample from Germany.

    PubMed

    Benecke, M; Knopf, M; Voll, W; Oesterreich, W; Jacobi, Y; Edelmann, J

    1998-10-01

    Applied DNA typing in medico-legal investigations, in criminalistic practice, and in paternity cases often relies on high inclusion and exclusion probabilities. For that reason, the short autosomal tandem repeat locus D8D306 was validated for forensic use and incorporated into a nonoverlapping multiplex reaction with HUMDHFRP2 and HUMCD4: The allele frequencies of D8S306 in four different regions of Germany (n = 1220 alleles) were determined for use in a population database; the allele distributions did not significantly deviate from each other. The hererozygosity of D8S306 is 83%, expected exclusion chance in stain cases is 96% (paternity cases: 69%), the lowest amount of successfully amplified DNA was 30 pg. The alleles are in Hardy-Weinberg equilibrium. PMID:9820956

  16. Are variable-number tandem repeats appropriate for genotyping Mycobacterium leprae?

    PubMed

    Monot, Marc; Honoré, Nadine; Balière, Charlotte; Ji, Baohong; Sow, Samba; Brennan, Patrick J; Cole, Stewart T

    2008-07-01

    Comparative genomics analysis of the Tamil Nadu strain of Mycobacterium leprae has uncovered several polymorphic sites with potential as epidemiological tools. In this study we compared the stability of two different markers of genomic biodiversity of M. leprae in several biopsy samples isolated from the same leprosy patient. The first type comprises five different variable-number tandem repeats (VNTR), while the second is composed of three single nucleotide polymorphisms (SNP). Contrasting results were obtained, since no variation was seen in the SNP profiles of M. leprae from 42 patients from 7 different locations in Mali whereas the VNTR profiles varied considerably. Furthermore, since variation in the VNTR pattern was seen not only between different isolates of M. leprae but also between biopsy samples from the same patient, these VNTR may be too dynamic for use as epidemiological markers for leprosy. PMID:18495858

  17. Multilocus variable-number tandem-repeat analysis of Neisseria meningitidis serogroup C in China.

    PubMed

    Shan, X Y; Zhou, H J; Zhang, J; Zhu, B Q; Xu, L; Xu, Z; Hu, G C; Bai, A Y; Shi, Y W; Jiang, B F; Shao, Z J

    2015-10-01

    This study characterized Neisseria meningitidis serogroup C strains in China in order to establish their genetic relatedness and describe the use of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) to provide useful epidemiological information. A total of 215 N. meningitidis serogroup C strains, obtained from 2003 to 2012 in China, were characterized by MLVA with different published schemes as well as multilocus sequence typing. (i) Based on the MLVA scheme with a combination of five highly variable loci, 203 genotypes were identified; this level of discrimination supports its use for resolving closely related isolates. (ii) Based on a combination of ten low variable loci, clear phylogenetic relationships were established within sequence type complexes. In addition, there was evidence of microevolution of VNTR loci over the decade as strain lineages spread from Anhui to other provinces, the more distant the provinces from Anhui, the higher the genetic variation. PMID:25778999

  18. A continuous linkage map of 22 short tandem repeat polymorphisms on human chromosome 12

    SciTech Connect

    Dawson, E.; Shaikh, S.; Powell, J.F.; Gill, M. ); Weber, J.L.; Wang, Z. ); Weissenbach, J. )

    1993-07-01

    A continuous linkage map consisting of 22 short tandem repeat polymorphisms has been constructed for human chromosome 12 using 23 non-CEPH pedigrees. The markers were distributed at an average distance of 9.35 cM (3.1-33.9 cM). Eighteen of the markers could be positioned uniquely with a likelihood of >1000:1. The physical locations of some of the markers suggest that the map covers 85-95% of the chromosome. This framework map of 18 markers has a female length of 213 cM and a male length of 131 cM. Female recombination frequencies were greater than male recombination frequencies except in the distal portion of the short arm. The map provides confirmatory evidence for orders established previously on CEPH pedigrees and uniquely positions 4 additional markers (CD4, ATPSB, D12S56, PLA2). 19 refs., 1 fig., 1 tab.

  19. Success Rates of Nuclear Short Tandem Repeat Typing from Different Skeletal Elements

    PubMed Central

    Miloš, Ana; Selmanović, Arijana; Smajlović, Lejla; Huel, René L.M.; Katzmarzyk, Cheryl; Rizvić, Adi; Parsons, Thomas J.

    2007-01-01

    Aim To evaluate trends in DNA typing success rates of different skeletal elements from mass graves originating from conflicts that occurred in the former Yugoslavia (Bosnia and Herzegovina and Kosovo) during the 1990s, and to establish correlation between skeletal sample age and success of high throughput short tandem repeat (STR) typing in the large data set of the International Commission on Missing Persons. Method DNA extraction and short tandem repeat (STR) typing have been attempted on over 25 000 skeletal samples. The skeletal samples originated from different geographical locations where the conflicts occurred and from different time periods from 1992 to 1999. DNA preservation in these samples was highly variable, but was often significantly degraded and of limited quantity. For the purpose of this study, processed samples were categorized according to skeletal sample type, sample age since death, and success rates tabulated. Results Well-defined general trends in success rates of DNA analyses were observed with respect to the type of bone tested and sample age. The highest success rates were observed with samples from dense cortical bone of weight-bearing leg bones (femur 86.9%), whereas long bones of the arms showed significantly lower success (humerus 46.2%, radius 24.5%, ulna 22.8%). Intact teeth also exhibited high success rates (teeth 82.7%). DNA isolation from other skeletal elements differed considerably in success, making bone sample selection an important factor influencing success. Conclusion The success of DNA typing is related to the type of skeletal sample. By carefully evaluating skeletal material available for forensic DNA testing with regard to sample age and type of skeletal element available, it is possible to increase the success and efficiency of forensic DNA testing. PMID:17696303

  20. Population data for 17 short tandem repeat loci on Y chromosome in northern Croatia.

    PubMed

    Gršković, Branka; Mršić, Gordan; Polašek, Ozren; Vrdoljak, Andro; Merkaš, Siniša; Anđelinović, Simun

    2011-03-01

    Human Y-short tandem repeats (STRs) are tandem repeat arrays of two to seven base pair units on non-recombining region (NRY) of the human Y chromosome. Studies on Y-STR are interesting in both population genetics and forensics. The aim of this study was to investigate the population genetic properties of 17 STR loci on Y chromosome in the northern Croatia region. We carried out a statistical analysis of the data from previously performed genetic analysis collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 220 unrelated healthy men from northern Croatia were selected for the purpose of this study. Genomic DNA was extracted using Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 210 haplotypes were identified, 200 of which were unique. Total haplotype diversity was 0.995. Locus diversity varied from 0.331 for DYS392 to 0.783 for DYS385 locus. Allele frequencies diversity was 0.662. Discrimination capacity was 95.7%. The use of European minimal haplotype set indicated the most resemblance of this population to the Croatian capital of Zagreb, with modest resemblance to Bosnia and Herzegovina, Serbia and Hungary. This article provides the first overview of the Y chromosome STR variability in northern Croatia, thus providing the referent point for any future forensic and genetic epidemiology efforts in this region. PMID:20859689

  1. Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning

    PubMed Central

    2011-01-01

    Background Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. The histone H3 variant CENH3 (centromeric histone H3) is viewed as the key element of centromere chromatin and its interaction with centromere DNA is epigenetic in that its localization to centromeres is not sequence-dependent. Results In order to investigate what influence the DNA sequence exerts on CENH3 chromatin structure, we examined CENH3 nucleosome footprints on maize centromere DNA. We found a predominant average nucleosome spacing pattern of roughly 190-bp intervals, which was also the dominant arrangement for nucleosomes genome-wide. For CENH3-containing nucleosomes, distinct modes of nucleosome positioning were evident within that general spacing constraint. Over arrays of the major ~156-bp centromeric satellite sequence (tandem repeat) CentC, nucleosomes were not positioned in register with CentC monomers but in conformity with a striking ~10-bp periodicity of AA/TT dimers within the sequence. In contrast, nucleosomes on a class of centromeric retrotransposon (CRM2) lacked a detectable AA/TT periodicity but exhibited tightly phased positioning. Conclusions These data support a model in which general chromatin factors independent of both DNA sequence and CENH3 enforce roughly uniform centromeric nucleosome spacing while allowing flexibility in the mode in which nucleosomes are positioned. In the case of tandem repeat DNA, the natural bending effects related to AA/TT periodicity produce an energetically-favourable arrangement consistent with conformationally rigid nucleosomes and stable chromatin at centromeres. PMID:21352520

  2. Exceptionally long 5' UTR short tandem repeats specifically linked to primates.

    PubMed

    Namdar-Aligoodarzi, P; Mohammadparast, S; Zaker-Kandjani, B; Talebi Kakroodi, S; Jafari Vesiehsari, M; Ohadi, M

    2015-09-10

    We have previously reported genome-scale short tandem repeats (STRs) in the core promoter interval (i.e. -120 to +1 to the transcription start site) of protein-coding genes that have evolved identically in primates vs. non-primates. Those STRs may function as evolutionary switch codes for primate speciation. In the current study, we used the Ensembl database to analyze the 5' untranslated region (5' UTR) between +1 and +60 of the transcription start site of the entire human protein-coding genes annotated in the GeneCards database, in order to identify "exceptionally long" STRs (≥5-repeats), which may be of selective/adaptive advantage. The importance of this critical interval is its function as core promoter, and its effect on transcription and translation. In order to minimize ascertainment bias, we analyzed the evolutionary status of the human 5' UTR STRs of ≥5-repeats in several species encompassing six major orders and superorders across mammals, including primates, rodents, Scandentia, Laurasiatheria, Afrotheria, and Xenarthra. We introduce primate-specific STRs, and STRs which have expanded from mouse to primates. Identical co-occurrence of the identified STRs of rare average frequency between 0.006 and 0.0001 in primates supports a role for those motifs in processes that diverged primates from other mammals, such as neuronal differentiation (e.g. APOD and FGF4), and craniofacial development (e.g. FILIP1L). A number of the identified STRs of ≥5-repeats may be human-specific (e.g. ZMYM3 and DAZAP1). Future work is warranted to examine the importance of the listed genes in primate/human evolution, development, and disease. PMID:26022613

  3. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching.

    PubMed

    Someswara Rao, Chinta; Raju, S Viswanadha

    2016-03-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching. PMID:26981434

  4. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    PubMed Central

    Someswara Rao, Chinta; Raju, S. Viswanadha

    2016-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching. PMID:26981434

  5. Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci.

    PubMed

    Li, Shi-Lin; Yamamoto, Toshimichi; Yoshimoto, Takashi; Uchihi, Rieko; Mizutani, Masaki; Kurimoto, Yukihide; Tokunaga, Katsushi; Jin, Feng; Katsumata, Yoshinao; Saitou, Naruya

    2006-02-01

    We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2-6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K> or =3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed. PMID:16315063

  6. A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes.

    PubMed

    Hauck, Yolande; Soler, Charles; Gérôme, Patrick; Vong, Rithy; Macnab, Christine; Appere, Géraldine; Vergnaud, Gilles; Pourcel, Christine

    2015-07-01

    Propionibacterium acnes plays a central role in the pathogenesis of acne and is responsible for severe opportunistic infections. Numerous typing schemes have been developed that allow the identification of phylotypes, but they are often insufficient to differentiate subtypes. To better understand the genetic diversity of this species and to perform epidemiological analyses, high throughput discriminant genotyping techniques are needed. Here we describe the development of a multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) method. Thirteen VNTRs were identified in the genome of P. acnes and were used to genotype a collection of clinical isolates. In addition, publically available sequencing data for 102 genomes were analyzed in silico, providing an MLVA genotype. The clustering of MLVA data was in perfect congruence with whole genome based clustering. Analysis of the clustered regularly interspaced short palindromic repeat (CRISPR) element uncovered new spacers, a supplementary source of genotypic information. The present MLVA13 scheme and associated internet database represents a first line genotyping assay to investigate large number of isolates. Particular strains may then be submitted to full genome sequencing in order to better analyze their pathogenic potential. PMID:25965840

  7. Variability of the tandem repeat region of the Escherichia coli tolA gene.

    PubMed

    Zhou, Kai; Vanoirbeek, Kristof; Aertsen, Abram; Michiels, Chris W

    2012-06-01

    An intragenic tandem repeat (TR) region has been previously reported in the tolA gene of Escherichia coli. In silico analysis of 123 E. coli tolA sequences from Genbank and PCR analysis of the tolA TR region from 111 additional E. coli strains revealed that this TR region is highly variable. Nine different TR sizes with 8 up to 16 repeat units were found in in silico analysis and 6 of these were also found by PCR analysis. The 13-unit TR emerged as the predominant type using both approaches (47.2% and 86.5%, respectively). Remarkably, TRs in pathogenic strains appeared to be more variable than those in non-pathogens. To demonstrate the occurrence of TR variation in a clonal population, a selection system for TR deletion events was constructed by inserting the 13-unit TR region of MG1655 in frame into a plasmid-borne chloramphenicol acetyltransferase (cat) gene. The resulting cat gene no longer conferred chloramphenicol resistance unless the insert size was reduced by TR contraction. Using this system, Cm-resistant revertants with a TR contraction were recovered at a frequency of 1.1 × 10(-7), and contraction was shown to be recA-dependent and enhanced in a DNA repair-deficient mutS background. PMID:22659144

  8. Diversity in a Variable-Number Tandem Repeat from Yersinia pestis

    PubMed Central

    Adair, D. M.; Worsham, P. L.; Hill, K. K.; Klevytska, A. M.; Jackson, P. J.; Friedlander, A. M.; Keim, P.

    2000-01-01

    We have identified a tetranucleotide repeat sequence, (CAAA)N, in the genome of Yersinia pestis, the causative agent of plague. This variable-number tandem repeat (VNTR) region has nine alleles and great diversity (calculated as 1 minus the sum of the squared allele frequencies) (diversity value, 0.82) within a set of 35 diverse Y. pestis strains. In contrast, the nucleotide sequence of the lcrV (low-calcium-response) gene differed only slightly among these strains, having a haplotype diversity value of 0.17. Replicated cultures, phenotypic variants of particular strains, and extensively cultured replicates within strains did not differ in VNTR allele type. Thus, while a high mutation rate must contribute to the great diversity of this locus, alleles appear stable under routine laboratory culture conditions. The classic three plague biovars did not have single identifying alleles, although there were allelic biases within biovar categories. The antiqua biovar was the most diverse, with four alleles observed in 5 strains, while the orientalis and mediaevalis biovars exhibited five alleles in 21 strains and three alleles in 8 strains, respectively. The CAAA VNTR is located immediately adjacent to the transcriptional promoters for flanking open reading frames and may affect their activity. This VNTR marker may provide a high-resolution tool for epidemiological analyses of plague. PMID:10747136

  9. Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast

    PubMed Central

    Noskov, Vladimir N.; Segall-Shapiro, Thomas H.; Chuang, Ray-Yuan

    2010-01-01

    The complete synthetic Mycoplasma genitalium genome (∼583 kb) has been assembled and cloned as a circular plasmid in the yeast Saccharomyces cerevisiae. Attempts to engineer the cloned genome by standard genetic methods involving the URA3/5-fluoroorotic acid (5-FOA) counter-selection have shown a high background of 5-FOA resistant clones derived from spontaneous deletions of the bacterial genome maintained in yeast. Here, we report a method that can seamlessly modify the bacterial genome in yeast with high efficiency. This method requires two sequential homologous recombination events. First, the target region is replaced with a mutagenesis cassette that consists of a knock-out CORE (an18-bp I-SceI recognition site, the SCEI gene under the control of the GAL1 promoter, and the URA3 marker) and a DNA fragment homologous to the sequence upstream of the target site. The replacement generates tandem repeat sequences flanking the CORE. Second, galactose induces the expression of I-SceI, which generates a double-strand break (DSB) at the recognition site. This DSB promotes intra-molecular homologous recombination between the repeat sequences, and leads to an excision of the CORE. As a result, a seamless modification is generated. This method can be adapted for a variety of genomic modifications and may provide an important tool to modify and design natural or synthetic genomes propagated in yeast. PMID:20228123

  10. Submegabase Clusters of Unstable Tandem Repeats Unique to the Tla Region of Mouse T Haplotypes

    PubMed Central

    Uehara, H.; Ebersole, T.; Bennett, D.; Artzt, K.

    1990-01-01

    We describe here the identification and genomic organization of mouse t haplotype-specific elements (TSEs) 7.8 and 5.8 kb in length. The TSEs exist as submegabase-long clusters of tandem repeats localized in the Tla region of the major histocompatibility complex of all t haplotype chromosomes examined. In contrast, no such clusters were detected among 12 inbred strains of Mus musculus and other Mus species; thus, clusters of TSEs represent the first absolutely qualitative difference between t haplotypes and wild-type chromosomes. Pulsed field gel electrophoresis shows that the number of clusters, and the number of repeats in each cluster are extremely variable. Dramatic quantitative differences of TSEs uniquely distinguish every independent t haplotype from any other. The complete nucleotide sequence of one 7.8-kb TSE reveals significant homology to the ETn (a major transcript in the early embryo of the mouse), and some homologies to intracisternal A-particles and the mammary tumor virus env gene. Apart from the diagnostic relevance to t haplotypes, evolutionary and functional significances are discussed with respect to chromosome structure and genetic recombination. PMID:2076812

  11. DNA Fingerprint Analysis of Three Short Tandem Repeat (STR) Loci for Biochemistry and Forensic Science Laboratory Courses

    ERIC Educational Resources Information Center

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C.; Alviri, Mahta; Ginty, Shannon; Love, John J.

    2006-01-01

    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek)…

  12. Core promoter short tandem repeats as evolutionary switch codes for primate speciation.

    PubMed

    Ohadi, Mina; Valipour, Elaheh; Ghadimi-Haddadan, Saeed; Namdar-Aligoodarzi, Pegah; Bagheri, Abouzar; Kowsari, Ali; Rezazadeh, Maryam; Darvish, Hossein; Kazeminasab, Somayeh

    2015-01-01

    Alteration in gene expression levels underlies many of the phenotypic differences across species. Because of their highly mutable nature, proximity to the +1 transcription start site (TSS), and the emerging evidence of functional impact on gene expression, core promoter short tandem repeats (STRs) may be considered an ideal source of variation across species. In a genome-scale analysis of the entire Homo sapiens protein-coding genes, we have previously identified core promoters with at least one STR of ≥ 6-repeats, with possible selective advantage in this species. In the current study, we performed reverse analysis of the entire Homo sapiens orthologous genes in mouse in the Ensembl database, in order to identify conserved STRs that have shrunk as an evolutionary advantage to humans. Two protocols were used to minimize ascertainment bias. Firstly, two species sharing a more recent ancestor with Homo sapiens (i.e. Pan troglodytes and Gorilla gorilla gorilla) were also included in the study. Secondly, four non-primate species encompassing the major orders across Mammals, including Scandentia, Laurasiatheria, Afrotheria, and Xenarthra were analyzed as out-groups. We introduce STR evolutionary events specifically identical in primates (i.e. Homo sapiens, Pan troglodytes, and Gorilla gorilla gorilla) vs. non-primate out-groups. The average frequency of the identically shared STR motifs across those primates ranged between 0.00005 and 0.06. The identified genes are involved in important evolutionary and developmental processes, such as normal craniofacial development (TFAP2B), regulation of cell shape (PALMD), learning and long-term memory (RGS14), nervous system development (GFRA2), embryonic limb morphogenesis (PBX2), and forebrain development (APAF1). We provide evidence of core promoter STRs as evolutionary switch codes for primate speciation, and the first instance of identity-by-descent for those motifs at the interspecies level. PMID:25099915

  13. Genetic analysis of a Sicilian population using 15 short tandem repeats.

    PubMed

    Calò, C M; Garofano, L; Mameli, A; Pizzamiglio, M; Vona, G

    2003-04-01

    The genetic structure of the population of Alia (Sicily, Italy) was analyzed using 15 short tandem repeats: TPOX, D2S1338, D3S1358, FIBRA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D19S433, and D21S11. Two of these markers, D2S1338 and D19S433, have never before been used in research on population genetics and only recently have they been put to use in forensic medicine. Results of the analysis underline the genetic isolation of the Alia population and show it to be a recent bottleneck as a consequence of a cholera epidemic in 1837. While comparing the Alia population with other populations from Sicily, a genetic heterogeneity within Sicily was uncovered, thus confirming previous results obtained from the analysis of classical markers. This heterogeneity underlines the existence of genetic boundaries within the island. Comparisons with other Italian, Mediterranean, and European populations highlight the differentiation of the Sicilian population, reflecting the presence of a genetic boundary that separates Sicily from northern and central Italy and from the western Mediterranean basin. PMID:12943156

  14. Diversity of Variable Number Tandem Repeat Loci in Shigella Species Isolated from Pediatric Patients

    PubMed Central

    Ranjbar, Reza; Memariani, Mojtaba; Memariani, Hamed

    2015-01-01

    Multilocus variable number tandem repeat (VNTR) analysis (MLVA) is a new typing method with several advantages compared to other methods. Dissemination of Shigella is highly significant in developing countries. Whilst Shigella is becoming increasingly important as an etiologic agent of pediatric shigellosis in Iran, little is known about the genetic diversity of the local strains. Therefore, the aim of this study was to describe the genetic diversity of Shigella species isolated from pediatric patients in Tehran, Iran. A total of 53 Shigella isolates were obtained from 1070 patients with diarrhea (less than 12 years of age). All isolates were identified by routine biochemical and serological tests. The confirmed Shigella isolates were further serogrouped (by the slide agglutination) using slide agglutination method. MLVA assay with the seven loci resolved 53 Shigella isolates into 36 different genotypes. Almost all the isolates were classified into five clonal complexes. Furthermore, our MLVA assay could effectively distinguish the four Shigella species. This study has provided valuable insights into the genetic heterogeneity of Shigella species in Tehran, Iran. Our findings can be helpful for further epidemiological surveillance of Shigella species in this country in the future. PMID:26629486

  15. Improvement of short tandem repeat analysis of samples highly contaminated by humic acid.

    PubMed

    Seo, Seung Bum; Jin, Hong Xuan; Lee, Hye Young; Ge, Jianye; King, Jonathan L; Lyoo, Sung Hee; Shin, Dong Hoon; Lee, Soong Deok

    2013-10-01

    We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick(®) PCR Purification, QIAamp(®) DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX(®) Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold(®) DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX(®) Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples. PMID:24112347

  16. Use of short tandem repeat analysis in unusual presentations of trophoblastic tumors and their mimics.

    PubMed

    Aranake-Chrisinger, John; Huettner, Phyllis C; Hagemann, Andrea R; Pfeifer, John D

    2016-06-01

    Gestational trophoblastic tumors can be difficult to distinguish from nongestational neoplasms. Somatic and germ cell tumors can mimic gestational choriocarcinoma, and epithelioid trophoblastic tumor (ETT) is known for its histologic, and sometimes clinical, resemblance to squamous cell carcinoma. Short tandem repeat (STR) analysis can separate gestational from nongestational neoplasms and can provide useful information about the type of causative conceptus. We present a series of cases which demonstrate the utility of STR analysis in the evaluation of gestational choriocarcinoma, epithelioid trophoblastic tumor, and their mimics. Samples from normal tissue and tumor were microdissected. DNA was extracted, and STR analysis was performed. Five cases were identified in which there was clinical and/or histologic concern for a gestational trophoblastic neoplasm. Case 1 is a choriocarcinoma presenting concurrently with a 16-week gestation. STR testing on the tumor, mother, and fetus showed that the tumor arose from a previous occult complete hydatidiform mole. Case 2 is an ETT presenting as multiple masses in bilateral kidneys, initially diagnosed as urothelial carcinoma. However, because of an elevated human chorionic gonadotropin, additional workup was performed which showed that the tumor was most likely an ETT. STR analysis showed that the tumor arose from a nonmolar pregnancy. Cases 3-5 illustrate somatic carcinomas mimicking gestational neoplasia. In those cases, STR confirmed a somatic origin. STR can be useful in distinguishing gestational from nongestational neoplasms, particularly in unusual settings. Also, STR analysis can add clinically useful information that is not available from clinical or histologic evaluation. PMID:26980014

  17. Genetic diversity of 17 Y-short tandem repeats in Indian population.

    PubMed

    Ghosh, Tania; Kalpana, D; Mukerjee, Sanjukta; Mukherjee, Meeta; Sharma, Anil Kumar; Nath, Subhankar; Rathod, Varsha Rajesh; Thakar, Mukesh Kumar; Jha, Ganga Nath

    2011-08-01

    Seventeen short tandem repeats (DYS389I, DYS390, DYS389II, DYS19, DYS385a/b, DYS393, DYS391, DYS392, DYS439, DYS438, DYS456, DYS458, DYS635, Y(GATA)H4, DYS437, and DYS448) from the non-recombining region of the human Y-chromosome were analyzed in 750 unrelated males representing four major linguistic families of India using AmpFlSTR(®) Yfiler(®) PCR Amplification kit. A total of 612 distinct haplotypes were observed, of which 545 were unique. Rare alleles for the loci DYS456, DYS458, DYS635, Y(GATA)H4, and duplication at the loci DYS389I and DYS389II were also observed. To understand the genetic diversity of the Indian population, and utility of Y-STRs in forensics, the locus diversity, haplotype diversity, and discrimination capacity in all populations was determined. MDS plot based on pairwise Φ(st) and AMOVA revealed the high genetic heterogeneity among the Indian populations due to linguistic diversity and social stratification. PMID:21277272

  18. Analysis of Y-chromosomal short tandem repeat (STR) polymorphism in an Iranian Sadat population.

    PubMed

    Rafiee, M R; Sokhansanj, A; Naghizadeh, M A; Farazmand, A

    2009-08-01

    The molecular genotyping of individuals and reconstruction of kinship through short and highly polymorphic DNA markers, so called short tandem repeats (STR), has become one of the important and efficient methods in anthropology studies and forensic science. Although many populations have been analyzed, no study has yet been carried out on Sadat populations who are putative descendents of Prophet Mohammad (peace be upon him). Polymorphisms of 6 Y-STR loci (DYS19, DYS385a/b, DYS389II, DYS390, DYS392, and DYS393) have been studied in an unrelated population of Sadat males. The aim of this study was to find possible similarities within Sadat males, resided in Iran. Among Sadat, DYS385b was proved to be the most polymorphic (GD = 0.8588), and DYS392 showed the lowest polymorphism (GD = 0.3527). In 50 samples, 45 different haplotypes were found, of which 39 haplotypes were unique. In the study, three samples had multi-allelic patterns. Haplotype diversity, in regard to these 7 markers was 0.9942. PMID:19769300

  19. Genetic individualization of Cannabis sativa by a short tandem repeat multiplex system.

    PubMed

    Mendoza, Maria A; Mills, DeEtta K; Lata, Hemant; Chandra, Suman; ElSohly, Mahmoud A; Almirall, Jose R

    2009-01-01

    Cannabis sativa is the most frequently used of all illicit drugs in the USA. Cannabis has been used throughout history for its stems in the production of hemp fiber, seed for oil and food, and buds and leaves as a psychoactive drug. Short tandem repeats (STRs) were chosen as molecular markers owing to their distinct advantages over other genetic methods. STRs are codominant, can be standardized such that reproducibility between laboratories can be easily achieved, have a high discrimination power, and can be multiplexed. In this study, six STR markers previously described for C. sativa were multiplexed into one reaction. The multiplex reaction was able to individualize 98 cannabis samples (14 hemp and 84 marijuana, authenticated as originating from 33 of the 50 states of the USA) and detect 29 alleles averaging 4.8 alleles per loci. The data did not relate the samples from the same state to each other. This is the first study to report a single-reaction sixplex and apply it to the analysis of almost 100 cannabis samples of known geographic origin. PMID:19066867

  20. Validation of a Short Tandem Repeat Multiplex Typing System for Genetic Individualization of Domestic Cat Samples

    PubMed Central

    Coomber, Nikia; David, Victor A.; O’Brien, Stephen J.; Menotti-Raymond, Marilyn

    2007-01-01

    Aim To conduct developmental validation studies on a polymerase chain reaction (PCR) based short tandem repeat (STR) multiplex typing system, developed for the purpose of genetic individualization and parentage testing in domestic cat samples. Methods To evaluate reproducibility of the typing system, the multiplex was amplified using DNA extracted from hair, blood, and buccal samples obtained from the same individual (n = 13). Additional studies were performed to evaluate the system’s species’ specificity, using 26 North American mammalian species and two prokaryotes Sacchromyces and Escherichia coli, sensitivity, and ability to identify DNA mixtures. Patterns of Mendelian inheritance and mutation rates for the 11 loci were directly examined in a large multi-generation domestic cat pedigree (n = 263). Results Our studies confirm that the multiplex system was species-specific for feline DNA and amplified robustly with as little as 125 picograms of genomic template DNA, demonstrating good product balance. The multiplex generated all components of a two DNA mixture when the minor component was one tenth of the major component at a threshold of 50 relative fluorescence units. The multiplex was reproducible in multiple tissue types of the same individual. Mutation rates for the 11 STR were within the range of sex averaged rates observed for Combined DNA Index System (CODIS) loci. Conclusion The cat STR multiplex typing system is a robust and reliable tool for the use of forensic DNA analysis of domestic cat samples. PMID:17696310

  1. Short tandem repeats haplotyping of the HLA region in preimplantation HLA matching.

    PubMed

    Fiorentino, Francesco; Kahraman, Semra; Karadayi, Hüseyin; Biricik, Anil; Sertyel, Semra; Karlikaya, Güvenc; Saglam, Yaman; Podini, Daniele; Nuccitelli, Andrea; Baldi, Marina

    2005-08-01

    Recently, preimplantation genetic diagnosis (PGD) has been considered for several indications beyond its original purpose, not only to test embryos for genetic disease but also to select embryos for a nondisease trait, such as specific human leukocyte antigen (HLA) genotypes, related to immune compatibility with an existing affected child in need of a haematopoetic stem cell (HSC) transplant. We have optimized an indirect single-cell HLA typing protocol based on a multiplex fluorescent polymerase chain reaction (PCR) of short tandem repeat (STR) markers scattered throughout the HLA complex. The assay was clinically applied in 60 cycles from 45 couples. A conclusive HLA-matching diagnosis was achieved in 483/530 (91.1%) of the embryos tested. In total, 74 (15.3%) embryos revealed an HLA match with the affected siblings, 55 (11.4%) of which resulted unaffected and 46 (9.5%) have been transferred to the patients. Nine pregnancies were achieved, five healthy HLA-matched children have already been delivered and cord blood HSCs, were transplanted to three affected siblings, resulting in a successful haematopoietic reconstruction. PMID:15886713

  2. Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing.

    PubMed

    Darby, Brian J; Erickson, Shay F; Hervey, Samuel D; Ellis-Felege, Susan N

    2016-07-01

    High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data. PMID:27386092

  3. Highly Discriminatory Variable-Number Tandem-Repeat Markers for Genotyping of Trichophyton interdigitale Strains

    PubMed Central

    Drira, Ines; Hadrich, Ines; Neji, Sourour; Mahfouth, Nedia; Trabelsi, Houaida; Sellami, Hayet; Makni, Fattouma

    2014-01-01

    Trichophyton interdigitale is the second most frequent cause of superficial fungal infections of various parts of the human body. Studying the population structure and genotype differentiation of T. interdigitale strains may lead to significant improvements in clinical practice. The present study aimed to develop and select suitable variable-number tandem-repeat (VNTR) markers for 92 clinical strains of T. interdigitale. On the basis of an analysis of four VNTR markers, four to eight distinct alleles were detected for each marker. The marker with the highest discriminatory power had eight alleles and a D value of 0.802. The combination of all four markers yielded a D value of 0.969 with 29 distinct multilocus genotypes. VNTR typing revealed the genetic diversity of the strains, identifying three populations according to their colonization sites. A correlation between phenotypic characteristics and multilocus genotypes was observed. Seven patients harbored T. interdigitale strains with different genotypes. Typing of clinical T. interdigitale samples by VNTR markers displayed excellent discriminatory power and 100% reproducibility. PMID:24989614

  4. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.

    PubMed

    Sun, Guangyun; McGarvey, Stephen T; Bayoumi, Riad; Mulligan, Connie J; Barrantes, Ramiro; Raskin, Salmo; Zhong, Yixi; Akey, Joshua; Chakraborty, Ranajit; Deka, Ranjan

    2003-01-01

    We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended. PMID:12529704

  5. DNA tandem repeat instability in the Escherichia coli chromosome is stimulated by mismatch repair at an adjacent CAG·CTG trinucleotide repeat.

    PubMed

    Blackwood, John K; Okely, Ewa A; Zahra, Rabaab; Eykelenboom, John K; Leach, David R F

    2010-12-28

    Approximately half the human genome is composed of repetitive DNA sequences classified into microsatellites, minisatellites, tandem repeats, and dispersed repeats. These repetitive sequences have coevolved within the genome but little is known about their potential interactions. Trinucleotide repeats (TNRs) are a subclass of microsatellites that are implicated in human disease. Expansion of CAG·CTG TNRs is responsible for Huntington disease, myotonic dystrophy, and a number of spinocerebellar ataxias. In yeast DNA double-strand break (DSB) formation has been proposed to be associated with instability and chromosome fragility at these sites and replication fork reversal (RFR) to be involved either in promoting or in preventing instability. However, the molecular basis for chromosome fragility of repetitive DNA remains poorly understood. Here we show that a CAG·CTG TNR array stimulates instability at a 275-bp tandem repeat located 6.3 kb away on the Escherichia coli chromosome. Remarkably, this stimulation is independent of both DNA double-strand break repair (DSBR) and RFR but is dependent on a functional mismatch repair (MMR) system. Our results provide a demonstration, in a simple model system, that MMR at one type of repetitive DNA has the potential to influence the stability of another. Furthermore, the mechanism of this stimulation places a limit on the universality of DSBR or RFR models of instability and chromosome fragility at CAG·CTG TNR sequences. Instead, our data suggest that explanations of chromosome fragility should encompass the possibility of chromosome gaps formed during MMR. PMID:21149728

  6. DNA tandem repeat instability in the Escherichia coli chromosome is stimulated by mismatch repair at an adjacent CAG·CTG trinucleotide repeat

    PubMed Central

    Blackwood, John K.; Okely, Ewa A.; Zahra, Rabaab; Eykelenboom, John K.; Leach, David R. F.

    2010-01-01

    Approximately half the human genome is composed of repetitive DNA sequences classified into microsatellites, minisatellites, tandem repeats, and dispersed repeats. These repetitive sequences have coevolved within the genome but little is known about their potential interactions. Trinucleotide repeats (TNRs) are a subclass of microsatellites that are implicated in human disease. Expansion of CAG·CTG TNRs is responsible for Huntington disease, myotonic dystrophy, and a number of spinocerebellar ataxias. In yeast DNA double-strand break (DSB) formation has been proposed to be associated with instability and chromosome fragility at these sites and replication fork reversal (RFR) to be involved either in promoting or in preventing instability. However, the molecular basis for chromosome fragility of repetitive DNA remains poorly understood. Here we show that a CAG·CTG TNR array stimulates instability at a 275-bp tandem repeat located 6.3 kb away on the Escherichia coli chromosome. Remarkably, this stimulation is independent of both DNA double-strand break repair (DSBR) and RFR but is dependent on a functional mismatch repair (MMR) system. Our results provide a demonstration, in a simple model system, that MMR at one type of repetitive DNA has the potential to influence the stability of another. Furthermore, the mechanism of this stimulation places a limit on the universality of DSBR or RFR models of instability and chromosome fragility at CAG·CTG TNR sequences. Instead, our data suggest that explanations of chromosome fragility should encompass the possibility of chromosome gaps formed during MMR. PMID:21149728

  7. Rapid generation of long tandem DNA repeat arrays by homologous recombination in yeast to study their function in mammalian genomes

    PubMed Central

    2011-01-01

    We describe here a method to rapidly convert any desirable DNA fragment, as small as 100 bp, into long tandem DNA arrays up to 140 kb in size that are inserted into a microbe vector. This method includes rolling-circle phi29 amplification (RCA) of the sequence in vitro and assembly of the RCA products in vivo by homologous recombination in the yeast Saccharomyces cerevisiae. The method was successfully used for a functional analysis of centromeric and pericentromeric repeats and construction of new vehicles for gene delivery to mammalian cells. The method may have general application in elucidating the role of tandem repeats in chromosome organization and dynamics. Each cycle of the protocol takes ~ two weeks to complete. PMID:21982381

  8. Detection of maternal DNA in umbilical cord plasma by fluorescent PCR amplification of short tandem repeat sequences.

    PubMed

    Bauer, M; Orescovic, I; Schoell, W M; Bianchi, D W; Pertl, B

    2001-09-01

    Recently, maternal DNA was detected in umbilical cord blood using PCR amplification of minisatellite sequences. The presence of maternal DNA was demonstrated in 1% to 100% of umbilical cord blood samples. The objective of this study was to determine the frequency of cord blood contamination by maternal genetic material. We used fluorescent PCR amplification of highly polymorphic short tandem repeat (STR) markers to detect maternal DNA in umbilical cord plasma. PMID:11708473

  9. Food-Grade Expression of d-Psicose 3-Epimerase with Tandem Repeat Genes in Bacillus subtilis.

    PubMed

    He, Weiwei; Mu, Wanmeng; Jiang, Bo; Yan, Xin; Zhang, Tao

    2016-07-20

    An integrative food-grade expression system with tandem repeat target genes was constructed for the expression of d-psicose 3-epimerase (DPEase; EC 5.1.3.30). The DPEase gene fused with the P43 promoter constituted an independent monomeric expression cassette. Multimers of the expression cassette were constructed in vitro using the isocaudamer strategy. The recombinant integration plasmids pDG-nDPE (n = 1, 2, 3), which contained one, two, or three consecutive P43-DPEase tandem repeats, were integrated into the genome of B. subtilis. Then, the antibiotic resistance gene was deleted by the Cre/lox system, and the food-grade recombinant B. subtilis 1A751-nDPE (n = 1, 2, 3) with integrated tandem repeats of the P43-DPEase expression cassette were generated. The specific activity of the B. subtilis 1A751-3DPE was the highest among the recombinant strains and was ∼2.2-fold that of the 1A751-1DPE strain. Under the optimal conditions, 8 g/L of freeze-dried enzyme powder could convert 20% d-fructose (300 g/L) into d-allulose after 1 h. PMID:27358033

  10. Geographic variation within a tandemly repeated mitochondrial DNA D-loop region of a North American freshwater fish, Pylodictis olivaris.

    PubMed

    Padhi, Abinash

    2014-03-15

    The present study reports the distribution of a 35-bp mitochondrial DNA (mtDNA) D-loop tandemly repeated sequence in the populations of a North American freshwater catfish, Pylodictis olivaris, and the important role of a past geological event in the phylogeographic pattern of this species. A total of 330 individuals of flathead catfish, representing 34 drainages throughout the species' native range in the United States, were collected. While more than 70% of individuals sampled from the Southeastern Gulf Coast drainages were characterized by the presence of a 35-bp mtDNA D-loop tandem repeat proximal to the 5' end, more than 95% of samples from the Mississippi River and its tributaries, as well as from the drainages of the Southwest Gulf Coast region, lack this tandem repeat. Concomitantly, phylogenetic analyses revealed the existence of two distinct matrilineal lineages (lineage I and II) of P. olivaris, which were estimated to have diverged from a common ancestor sometime between 0.70 and 2.05myr ago. While one lineage is comprised of samples from the Mississippi River and its tributaries and rivers draining to the Southwest Gulf Coast, the other lineage is comprised of samples from the Southeastern Gulf Coast drainages. Each lineage also has two sub-lineages, which also showed geographic specificity. PMID:24440244

  11. Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines.

    PubMed

    Zhang, Zhou; Zheng, Yinan; Zhang, Xu; Liu, Cong; Joyce, Brian Thomas; Kibbe, Warren A; Hou, Lifang; Zhang, Wei

    2016-02-01

    Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). However, little is known about the role of short tandem repeat polymorphisms (STRPs), a class of structural genetic variants, in regulating cytosine modifications. Utilizing the published data on the International HapMap Project lymphoblastoid cell lines (LCLs), we assessed the relationships between 721 STRPs and the modification levels of 283,540 autosomal CpG sites. Our findings suggest that, in contrast to the predominant cis-acting mode for SNP-based mQTL, STRPs are associated with cytosine modification levels in both cis-acting (local) and trans-acting (distant) modes. In local scans within the ±1 Mb windows of target CpGs, 21, 9, and 21 cis-acting STRP-based mQTL were detected in CEU (Caucasian residents from Utah, USA), YRI (Yoruba people from Ibadan, Nigeria), and the combined samples, respectively. In contrast, 139,420, 76,817, and 121,866 trans-acting STRP-based mQTL were identified in CEU, YRI, and the combined samples, respectively. A substantial proportion of CpG sites detected with local STRP-based mQTL were not associated with SNP-based mQTL, suggesting that STRPs represent an independent class of mQTL. Functionally, genetic variants neighboring CpG-associated STRPs are enriched with genome-wide association study (GWAS) loci for a variety of complex traits and diseases, including cancers, based on the National Human Genome Research Institute (NHGRI) GWAS Catalog. Therefore, elucidating these STRP-based mQTL in addition to SNP-based mQTL can provide novel insights into the genetic architectures of complex traits. PMID:26714498

  12. Genetic polymorphisms of 17 short tandem repeat loci on Y chromosome in central Croatian population.

    PubMed

    Gršković, Branka; Mršić, Gordan; Polašek, Ozren; Vrdoljak, Andro; Merkaš, Siniša; Anđelinović, Simun

    2011-06-01

    In forensic casework, Y-chromosome short tandem repeat (STR) haplotyping is used in human identification, paternity testing and sexual assault cases where Y-STRs provide a male-specific DNA profile. The aim of this study was to describe the genetic structure of Y chromosome in a central Croatian population. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 220 unrelated healthy men from central Croatia were selected for the purpose of this study. Genomic DNA was extracted using a Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 212 haplotypes were identified, 204 of which were unique. Total haplotype diversity was 0.993. Locus diversity varied from 0.325 for DYS392 to 0.786 for DYS385. Discrimination capacity was 92.7%. Allele frequencies diversity was 0.615. Intermediate alleles 17.2, 18.2 and 19.2 were found at DYS458 locus. A comparison with published data for the European minimal haplotype set showed the closest relationship to the Croatian capital of Zagreb and Bosnia and Herzegovina with significant genetic distance from Slovenia and Austria. The central Croatian population is now well characterized in terms of Y-chromosome STRs, thus providing a solid basis for further forensic and genetic epidemiology studies. PMID:21279707

  13. Tandem repeat recombinant proteins as potential antigens for the sero-diagnosis of Schistosoma mansoni infection.

    PubMed

    Kalenda, Yombo Dan Justin; Kato, Kentaro; Goto, Yasuyuki; Fujii, Yoshito; Hamano, Shinjiro

    2015-12-01

    The diagnosis of schistosome infection, followed by effective treatment and/or mass drug administration, is crucial to reduce the disease burden. Suitable diagnostic tests and field-applicable tools are required to sustain schistosomiasis control programs. We therefore assessed the potential of tandem repeat (TR) proteins for sero-diagnosis of Schistosoma mansoni infection using an experimental mouse model. TR genes in the genome of S. mansoni were searched in silico and 7 candidates, named SmTR1, 3, 8, 9, 10, 11 and 15, were selected. Total RNA was extracted from S. mansoni adult worms and eggs. Target TR genes were amplified, cloned, and the proteins were expressed in Escherichia coli competent cells. Female BALB/c mice were infected with 100 S. mansoni cercariae and sera were collected each week post-infection for 18 weeks. The levels of IgG antibodies to SmTR antigens were compared to those to soluble egg antigen (SEA) and to soluble worm antigen preparation (SWAP). Sera of infected mice reacted to all the antigens whereas those of naïve mice did not. IgG responses to SmTR1, 3, 9 and 10 were detected at the early stage of infection. Interestingly, antibodies reacting to SmTR3, 9, 10 and 15 dramatically decreased 4 weeks after treatment with praziquantel, while those against SEA and SWAP remained elevated. Our study suggests that TR proteins, especially SmTR10, may be suitable antigens for sero-diagnosis of infection by S. mansoni and are potential markers for monitoring and surveillance of schistosomiasis, including re-infection after treatment with praziquantel. PMID:26148816

  14. Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification.

    PubMed

    Nims, Raymond W; Sykes, Greg; Cottrill, Karin; Ikonomi, Pranvera; Elmore, Eugene

    2010-12-01

    The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification. PMID:20927602

  15. Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae

    PubMed Central

    Zhao, Zhixin; Guo, Cheng; Sutharzan, Sreeskandarajan; Li, Pei; Echt, Craig S.; Zhang, Jie; Liang, Chun

    2013-01-01

    Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among the 31 species, no significant correlation was detected between the TR density and genome size. Interestingly, green alga Chlamydomonas reinhardtii (42,059 bp/Mbp) and castor bean Ricinus communis (55,454 bp/Mbp) showed much higher TR densities than all other species (13,209 bp/Mbp on average). In the 29 land plants, including 22 dicots, 5 monocots, and 2 bryophytes, 5′-UTR and upstream intergenic 200-nt (UI200) regions had the first and second highest TR densities, whereas in the two green algae (C. reinhardtii and Volvox carteri) the first and second highest densities were found in intron and coding sequence (CDS) regions, respectively. In CDS regions, trinucleotide and hexanucleotide motifs were those most frequently represented in all species. In intron regions, especially in the two green algae, significantly more TRs were detected near the intron–exon junctions. Within intergenic regions in dicots and monocots, more TRs were found near both the 5′ and 3′ ends of genes. GO annotation in two green algae revealed that the genes with TRs in introns are significantly involved in transcriptional and translational processing. As the first systematic examination of TRs in plant and green algal genomes, our study showed that TRs displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation in plants and green algae. PMID:24192840

  16. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

    PubMed Central

    Ballantyne, Kaye N; Ralf, Arwin; Aboukhalid, Rachid; Achakzai, Niaz M; Anjos, Maria J; Ayub, Qasim; Balažic, Jože; Ballantyne, Jack; Ballard, David J; Berger, Burkhard; Bobillo, Cecilia; Bouabdellah, Mehdi; Burri, Helen; Capal, Tomas; Caratti, Stefano; Cárdenas, Jorge; Cartault, François; Carvalho, Elizeu F; Carvalho, Monica; Cheng, Baowen; Coble, Michael D; Comas, David; Corach, Daniel; D'Amato, Maria E; Davison, Sean; de Knijff, Peter; De Ungria, Maria Corazon A; Decorte, Ronny; Dobosz, Tadeusz; Dupuy, Berit M; Elmrghni, Samir; Gliwiński, Mateusz; Gomes, Sara C; Grol, Laurens; Haas, Cordula; Hanson, Erin; Henke, Jürgen; Henke, Lotte; Herrera-Rodríguez, Fabiola; Hill, Carolyn R; Holmlund, Gunilla; Honda, Katsuya; Immel, Uta-Dorothee; Inokuchi, Shota; Jobling, Mark A; Kaddura, Mahmoud; Kim, Jong S; Kim, Soon H; Kim, Wook; King, Turi E; Klausriegler, Eva; Kling, Daniel; Kovačević, Lejla; Kovatsi, Leda; Krajewski, Paweł; Kravchenko, Sergey; Larmuseau, Maarten H D; Lee, Eun Young; Lessig, Ruediger; Livshits, Ludmila A; Marjanović, Damir; Minarik, Marek; Mizuno, Natsuko; Moreira, Helena; Morling, Niels; Mukherjee, Meeta; Munier, Patrick; Nagaraju, Javaregowda; Neuhuber, Franz; Nie, Shengjie; Nilasitsataporn, Premlaphat; Nishi, Takeki; Oh, Hye H; Olofsson, Jill; Onofri, Valerio; Palo, Jukka U; Pamjav, Horolma; Parson, Walther; Petlach, Michal; Phillips, Christopher; Ploski, Rafal; Prasad, Samayamantri P R; Primorac, Dragan; Purnomo, Gludhug A; Purps, Josephine; Rangel-Villalobos, Hector; Rębała, Krzysztof; Rerkamnuaychoke, Budsaba; Gonzalez, Danel Rey; Robino, Carlo; Roewer, Lutz; Rosa, Alexandra; Sajantila, Antti; Sala, Andrea; Salvador, Jazelyn M; Sanz, Paula; Schmitt, Cornelia; Sharma, Anil K; Silva, Dayse A; Shin, Kyoung-Jin; Sijen, Titia; Sirker, Miriam; Siváková, Daniela; Škaro, Vedrana; Solano-Matamoros, Carlos; Souto, Luis; Stenzl, Vlastimil; Sudoyo, Herawati; Syndercombe-Court, Denise; Tagliabracci, Adriano; Taylor, Duncan; Tillmar, Andreas; Tsybovsky, Iosif S; Tyler-Smith, Chris; van der Gaag, Kristiaan J; Vanek, Daniel; Völgyi, Antónia; Ward, Denise; Willemse, Patricia; Yap, Eric PH; Yong, Rita YY; Pajnič, Irena Zupanič; Kayser, Manfred

    2014-01-01

    Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database. PMID:24917567

  17. Genome-wide analysis of tandem repeats in plants and green algae.

    PubMed

    Zhao, Zhixin; Guo, Cheng; Sutharzan, Sreeskandarajan; Li, Pei; Echt, Craig S; Zhang, Jie; Liang, Chun

    2014-01-01

    Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among the 31 species, no significant correlation was detected between the TR density and genome size. Interestingly, green alga Chlamydomonas reinhardtii (42,059 bp/Mbp) and castor bean Ricinus communis (55,454 bp/Mbp) showed much higher TR densities than all other species (13,209 bp/Mbp on average). In the 29 land plants, including 22 dicots, 5 monocots, and 2 bryophytes, 5'-UTR and upstream intergenic 200-nt (UI200) regions had the first and second highest TR densities, whereas in the two green algae (C. reinhardtii and Volvox carteri) the first and second highest densities were found in intron and coding sequence (CDS) regions, respectively. In CDS regions, trinucleotide and hexanucleotide motifs were those most frequently represented in all species. In intron regions, especially in the two green algae, significantly more TRs were detected near the intron-exon junctions. Within intergenic regions in dicots and monocots, more TRs were found near both the 5' and 3' ends of genes. GO annotation in two green algae revealed that the genes with TRs in introns are significantly involved in transcriptional and translational processing. As the first systematic examination of TRs in plant and green algal genomes, our study showed that TRs displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation in plants and green algae. PMID:24192840

  18. Genetic structure of the Azores Islands: a study using 15 autosomal short tandem repeat loci.

    PubMed

    Santos, Cristina; Alvarez, Luis; Aluja, Maria Pilar; Bruges-Armas, Jacome; Lima, Manuela

    2009-12-01

    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes. PMID:20102040

  19. Pathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches.

    PubMed

    Dodd, David W; Tomchick, Diana R; Corey, David R; Gagnon, Keith T

    2016-03-01

    Expansion of a GGGGCC/CCCCGG repeat sequence in the first intron of the C9ORF72 gene is a leading cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). In this combined disorder, called c9FTD/ALS, the expansion is bidirectionally transcribed into sense and antisense repeat RNA associated with disease. To better understand the role of C9ORF72 repeat RNA in molecular disease pathology, we determined crystal structures of a [(CCCCGG)3(CCCC)] model antisense repeat RNA to 1.47 Å resolution. The RNA structure was an A-form-like double helix composed of repeating and regularly spaced tandem C:C mismatch pairs that perturbed helical geometry and surface charge. Solution studies revealed a preference for A-form-like helical conformations as the repeat number increased. Results provide a structural starting point for rationalizing the contribution of repeat RNA to c9FTD/ALS molecular disease mechanisms and for developing molecules to target C9ORF72 repeat RNA as potential therapeutics. PMID:26878348

  20. GENETIC VARIATION IN RED RASPBERRIES (RUBUS IDAEUS L.; ROSACEAE) FROM SITES DIFFERING IN ORGANIC POLLUTANTS COMPARED WITH SYNTHETIC TANDEM REPEAT DNA PROBES

    EPA Science Inventory

    Two synthetic tandem repetitive DNA probes were used to compare genetic variation at variable-number-tandem-repeat (VNTR) loci among Rubus idaeus L. var. strigosus (Michx.) Maxim. (Rosaceae) individuals sampled at eight sites contaminated by pollutants (N = 39) and eight adjacent...

  1. EmsB, a tandem repeated multi-loci microsatellite, new tool to investigate the genetic diversity of Echinococcus multilocularis.

    PubMed

    Bart, J M; Knapp, J; Gottstein, B; El-Garch, F; Giraudoux, P; Glowatzki, M L; Berthoud, H; Maillard, S; Piarroux, R

    2006-09-01

    In order to explore the genetic diversity within Echinococcus multilocularis (E. multilocularis), the cestode responsible for the alveolar echinococcosis (AE) in humans, a microsatellite, composed of (CA) and (GA) repeats and designated EmsB, was isolated and characterized in view of its nature and potential field application. PCR-amplification with specific primers exhibited a high degree of size polymorphism between E. multilocularis and Echinococcus granulosus sheep (G1) and camel (G6) strains. Fluorescent-PCR was subsequently performed on a panel of E. multilocularis isolates to assess intra-species polymorphism level. EmsB provided a multi-peak profile, characterized by tandemly repeated microsatellite sequences in the E. multilocularis genome. This "repetition of repeats" feature provided to EmsB a high discriminatory power in that eight clusters, supported by bootstrap p-values larger than 95%, could be defined among the tested E. multilocularis samples. We were able to differentiate not only the Alaskan from the European samples, but also to detect different European isolate clusters. In total, 25 genotypes were defined within 37 E. multilocularis samples. Despite its complexity, this tandem repeated multi-loci microsatellite possesses the three important features for a molecular marker, i.e. sensitivity, repetitiveness and discriminatory power. It will permit assessing the genetic polymorphism of E. multilocularis and to investigate its spatial distribution in detail. PMID:16504596

  2. Y-Short Tandem Repeat Multiplex Systems - Y-PLEX™ 6 and Y-PLEX™ 5.

    PubMed

    Shewale, J G

    2003-07-01

    Y-Chromosome short tandem repeats (Y-STRs) have become a very useful tool in forensic casework, paternity, and male lineage studies. In forensic casework, one can obtain the male profile from a mixture sample containing male and female DNA. Two Y-STR genotyping systems, Y-PLEX™ 6 and Y-PLEX™ 5, have been developed for use in human identification. Y-PLEX™ 6 enables simultaneous amplification of DYS393, DYS19, DYS389II, DYS390, DYS391, and DYS385; Y-PLEX™ 5 enables simultaneous amplification of DYS389I, DYS389II, DYS439, DYS438, and DYS392 loci. The Y-PLEX™ 6 and Y-PLEX™ 5 systems together provide analysis of all nine Y-STR loci generating minimal haplotype and two additional loci, DYS438 and DYS439. These systems also provide analysis for all 11 Y-STR loci recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM) for forensic casework and population database studies. Both the systems were validated following the Federal Bureau of Investigation (FBI) Director's Quality Assurance Standards. Allelic ladders, which serve as a reference in genotyping, were generated. The nucleotide sequence of alleles in the allelic ladder was determined and the nomenclature is in accord with the recommendations of the International Society of Forensic Genetics (ISFG). The minimum sensitivity of the Y-PLEX™ 6 and Y-PLEX™ 5 systems was 0.2 and 0.1 ng of male DNA, respectively. The nonhuman study revealed that the primers in the Y-PLEX™ 6 and Y-PLEX™ 5 systems were specific for the DNA from humans and some higher primates. Mean stutter values ranged from 3.6 to 11.9%. The Y-PLEX™ 6 and Y-PLEX™ 5 systems were used in several forensic cases. The results from these multiplex systems have been admitted in various U.S. Courts. Thus, Y-PLEX™ 6 and Y-PLEX™ 5 genotyping systems are sensitive, reliable, and robust for use in human forensic and male lineage identification studies. PMID:26256728

  3. Multilocus variable-number of tandem repeat analysis (MLVA) for Clostridium tyrobutyricum strains isolated from cheese production environment.

    PubMed

    Nishihara, Masaharu; Takahashi, Hajime; Sudo, Tomoko; Kyoi, Daisuke; Kawahara, Toshio; Ikeuchi, Yoshihiro; Fujita, Takashi; Kuda, Takashi; Kimura, Bon; Yanahira, Shuichi

    2014-11-01

    Clostridium tyrobutyricum is a gram-positive spore-forming anaerobe that is considered as the main causative agent for late blowing in cheese due to butyric acid fermentation. In this study, multilocus variable-number of tandem repeat (VNTR) analysis (MLVA) for C. tyrobutyricum was developed to identify the source of contamination by C. tyrobutyricum spores in the cheese production environment. For each contig constructed from the results of a whole genome draft sequence of C. tyrobutyricum JCM11008(T) based on next-generation sequencing, VNTR loci that were effective for typing were searched using the Tandem Repeat Finder program. Five VNTR loci were amplified by polymerase chain reaction (PCR) to determine their number of repeats by sequencing, and MLVA was conducted. 25 strains of C. tyrobutyricum isolated from the environment, raw milk, and silage were classified into 18 MLVA types (DI=0.963). Of the C. tyrobutyricum strains isolated from raw milk, natural cheese, and blown processed cheese, strains with identical MLVA type were detected, which suggested that these strains might have shifted from natural cheese to blown processed cheese. MLVA could be an effective tool for monitoring contamination of natural cheese with C. tyrobutyricum in the processed cheese production environment because of its high discriminability, thereby allowing the analyst to trace the source of contamination. PMID:25190602

  4. Replicational release of geminivirus genomes from tandemly repeated copies: evidence for rolling-circle replication of a plant viral DNA.

    PubMed

    Stenger, D C; Revington, G N; Stevenson, M C; Bisaro, D M

    1991-09-15

    Agrobacterium-mediated inoculation of Nicotiana benthamiana plants with Ti plasmids containing tandem genome repeats derived from different strains of the gemini-virus beet curly top virus (BCTV) resulted in the production of unit-length recombinant progeny genomes in systemically infected plants. When two putative plus-strand origins of replication were present in constructs used as inocula, a replicational escape mechanism was favored that resulted in progeny genomes of a single predominant genotype. The genotype was dependent upon the arrangement of repeated parental genomes in the inocula. Sequencing across the junction between parental BCTV strains in the recombinant progeny allowed mapping of the plus-strand origin of replication to a 20-base-pair sequence within the conserved hairpin found in all geminivirus genomes. In contrast, when inocula contained tandemly repeated BCTV genome sequences but only a single conserved hairpin, a number of different progeny genotypes were simultaneously replicated in infected plants, a result expected if unit-length viral genomes were generated by random intramolecular recombination events. These results and other considerations indicate that geminivirus DNA replication occurs by a rolling-circle mechanism. PMID:1896448

  5. Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

    SciTech Connect

    Jackson, P.J.; Walthers, E.A.; Richmond, K.L.

    1997-04-01

    PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.

  6. Genotyping the GGGCGG Tandem Repeat Promoter Polymorphism in the 5-Lipoxygenase Enzyme Gene (ALOX5) by Pyrosequencing Assay

    PubMed Central

    Schentrup, Anzeela M.; Allayee, Hooman; Lima, John J.; Johnson, Julie A.

    2009-01-01

    Aims: Efficient genotyping methods for many biologically significant repeat genetic polymorphisms, particularly in GC-rich regions of the genome, are limited. In particular, a short tandem repeat polymorphism [GGCGGG] in the promoter region of ALOX5 has been implicated as an important marker for inflammatory diseases. We developed a pyrosequencing assay to genotype the ALOX5 short tandem repeat polymorphism using pyrosequencing technology that will make assessing this important genetic marker in large, diverse populations more accessible than using current methods. Materials and Methods: We used a nested polymerase chain reaction approach to amplify DNA for pyrosequencing. Population allele frequencies were assessed in two cohorts of previously collected human DNA samples with 188 and 1032 samples, respectively. Sixteen genetic samples with known genotypes were used to confirm the accuracy of the method. Results and Discussion: Genotypes were 100% concordant with samples of known genotype. Genotype frequencies in European American, Hispanic, and African American agreed with previously published results (wild-type homozygotes 66%, 64%, and 19%, respectively). The method presented here will facilitate both genetic association and pharmacogenomic research on this polymorphism in large samples that are ethnically and/or racially admixed. PMID:19473080

  7. ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections

    PubMed Central

    Chindelevitch, Leonid; Colijn, Caroline; Moodley, Prashini; Wilson, Douglas; Cohen, Ted

    2016-01-01

    Genomic tools have revealed genetically diverse pathogens within some hosts. Within-host pathogen diversity, which we refer to as “complex infection”, is increasingly recognized as a determinant of treatment outcome for infections like tuberculosis. Complex infection arises through two mechanisms: within-host mutation (which results in clonal heterogeneity) and reinfection (which results in mixed infections). Estimates of the frequency of within-host mutation and reinfection in populations are critical for understanding the natural history of disease. These estimates influence projections of disease trends and effects of interventions. The genotyping technique MLVA (multiple loci variable-number tandem repeats analysis) can identify complex infections, but the current method to distinguish clonal heterogeneity from mixed infections is based on a rather simple rule. Here we describe ClassTR, a method which leverages MLVA information from isolates collected in a population to distinguish mixed infections from clonal heterogeneity. We formulate the resolution of complex infections into their constituent strains as an optimization problem, and show its NP-completeness. We solve it efficiently by using mixed integer linear programming and graph decomposition. Once the complex infections are resolved into their constituent strains, ClassTR probabilistically classifies isolates as clonally heterogeneous or mixed by using a model of tandem repeat evolution. We first compare ClassTR with the standard rule-based classification on 100 simulated datasets. ClassTR outperforms the standard method, improving classification accuracy from 48% to 80%. We then apply ClassTR to a sample of 436 strains collected from tuberculosis patients in a South African community, of which 92 had complex infections. We find that ClassTR assigns an alternate classification to 18 of the 92 complex infections, suggesting important differences in practice. By explicitly modeling tandem repeat

  8. ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections.

    PubMed

    Chindelevitch, Leonid; Colijn, Caroline; Moodley, Prashini; Wilson, Douglas; Cohen, Ted

    2016-02-01

    Genomic tools have revealed genetically diverse pathogens within some hosts. Within-host pathogen diversity, which we refer to as "complex infection", is increasingly recognized as a determinant of treatment outcome for infections like tuberculosis. Complex infection arises through two mechanisms: within-host mutation (which results in clonal heterogeneity) and reinfection (which results in mixed infections). Estimates of the frequency of within-host mutation and reinfection in populations are critical for understanding the natural history of disease. These estimates influence projections of disease trends and effects of interventions. The genotyping technique MLVA (multiple loci variable-number tandem repeats analysis) can identify complex infections, but the current method to distinguish clonal heterogeneity from mixed infections is based on a rather simple rule. Here we describe ClassTR, a method which leverages MLVA information from isolates collected in a population to distinguish mixed infections from clonal heterogeneity. We formulate the resolution of complex infections into their constituent strains as an optimization problem, and show its NP-completeness. We solve it efficiently by using mixed integer linear programming and graph decomposition. Once the complex infections are resolved into their constituent strains, ClassTR probabilistically classifies isolates as clonally heterogeneous or mixed by using a model of tandem repeat evolution. We first compare ClassTR with the standard rule-based classification on 100 simulated datasets. ClassTR outperforms the standard method, improving classification accuracy from 48% to 80%. We then apply ClassTR to a sample of 436 strains collected from tuberculosis patients in a South African community, of which 92 had complex infections. We find that ClassTR assigns an alternate classification to 18 of the 92 complex infections, suggesting important differences in practice. By explicitly modeling tandem repeat evolution

  9. Molecular characterization of Leptospira sp by multilocus variable number tandem repeat analysis (MLVA) from clinical samples: a case report.

    PubMed

    Pailhoriès, Hélène; Buzelé, Rodolphe; Picardeau, Mathieu; Robert, Sylvie; Mercier, Emmanuelle; Mereghetti, Laurent; Lanotte, Philippe

    2015-08-01

    Leptospirosis is a zoonotic infection for which diagnosis is difficult. It has appeared as a global emerging infectious disease over recent years. Genotype determination often requires a Leptospira strain obtained by culture, which is a long and fastidious technique. A method based on multilocus variable number tandem repeat analysis (MLVA) to determine the genotype of Leptospira interrogans, performed directly on blood or urine samples, is proposed. This method was applied to a fatal case of leptospirosis for which the geographical origin of infection was unknown. This technique will allow a genotype to be obtained for L. interrogans, even when cultures remain negative. PMID:26159846

  10. Increased Length of Long Terminal Repeats Inhibits Ty1 Transposition and Leads to the Formation of Tandem Multimers

    PubMed Central

    Lauermann, V.; Hermankova, M.; Boeke, J. D.

    1997-01-01

    The Ty1 retrotransposon of Saccharomyces cerevisiae is bounded by long-terminal repeats (LTRs). We have constructed a variety of Ty1 elements in which the LTR length has been increased from the normal length of 334 bp to >2 kb. Although small insertions in the LTR have minimal effects on transposition frequency, larger insertions dramatically reduce it. Nevertheless, elements with long LTRs are incorporated into the genome at a low frequency. Most of these rare insertion events represent Ty1 tandem (head to tail) multimers. PMID:9093846

  11. An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon).

    PubMed

    Ba, Hengxing; Wu, Lang; Liu, Zongyue; Li, Chunyi

    2016-01-01

    Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift. PMID:24621225

  12. Intrachromosomal tandem duplication and repeat expansion during attempts to inactivate the subtelomeric essential gene GSH1 in Leishmania

    PubMed Central

    Mukherjee, Angana; Langston, Lance D.; Ouellette, Marc

    2011-01-01

    Gamma-glutamylcysteine synthetase encoded by GSH1 is the rate-limiting enzyme in the biosynthesis of glutathione and trypanothione in Leishmania. Attempts to generate GSH1 null mutants by gene disruption failed in Leishmania infantum. Removal of even a single allele invariably led to the generation of an extra copy of GSH1, maintaining two intact wild-type alleles. In the second and even third round of inactivation, the markers integrated at the homologous locus but always preserved two intact copies of GSH1. We probed into the mechanism of GSH1 duplication. GSH1 is subtelomeric on chromosome 18 and Southern blot analysis indicated that a 10-kb fragment flanked by 466-bp direct repeated sequences was duplicated in tandem on the same chromosomal allele each time GSH1 was targeted. Polymerase chain reaction analysis and sequencing confirmed the generation of novel junctions created at the level of the 466-bp repeats consequent to locus duplication. In loss of heterozygosity attempts, the same repeated sequences were utilized for generating extrachromosomal circular amplicons. Our results are consistent with break-induced replication as a mechanism for the generation of this regional polyploidy to compensate for the inactivation of an essential gene. This chromosomal repeat expansion through repeated sequences could be implicated in locus duplication in Leishmania. PMID:21693561

  13. Development of a tandem repeat-based multilocus typing system distinguishing Babesia bovis geographic isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mini and microsatellite sequences have proven to be excellent tools for the differentiation of strains and populations in several protozoan parasites due to their high variability. In the present work we have searched the genome of the tick-transmitted bovine hemoprotozoon Babesia bovis for tandem r...

  14. Genotyping of Klebsiella Pneumonia Strains Isolated from Eldly Inpatients by Multiple-locus Variable-number Tandem-repeat Analysis.

    PubMed

    Zhang, Yuan-Yuan; Xu, Ya-Ping; DU, Peng-Cheng; Qiang, Yu-Jun; Zhang, Wen; Chen, Chen; Yu, Ji-Hong; Guo, Jun

    2016-08-01

    Objective To investigate the genotype of klebsiella pneumonia strains isolated from eldly inpatients by multiple-locus variable-number tandem-repeat analysis. Methods Totally 184 klebsiella pneumonia strains,isolated from eldly inpatients,were collected,and their genome DNA were extracted. The polymorphism of 7 variable-number tandem-repeat locus in the DNA samples was analyzed by multiple primers polymerase chain reaction and capillary electrophoresis. The clustering analysis of genotyping was carried out with the BioNumerics 5.1 software. Results A total of 139 genotypes were identified in 184 klebsiella pneumonia clinical strains,showing obvious genetic polymorphisms. With clustering analysis of genotypes,all the strains were categorized into three gene clusters (genogroups 1,2,and 3). The genogroup 1 was the biggest cluster,containing 93.06% of the isolated strains. Conclusion There was a predominant cluster in the klebsiella pneumonia strains isolated from eldly inpatients in our center,and the major source of klebsiella pneumonia infection remained the nosocomial infection. PMID:27594157

  15. Chromosomal mapping of tandem repeats in the Yesso Scallop, Patinopecten yessoensis (Jay, 1857), utilizing fluorescence in situ hybridization

    PubMed Central

    Li, Xuan; Yang, Zujing; Liao, Huan; Zhang, Zhengrui; Huang, Xiaoting; Bao, Zhenmin

    2016-01-01

    Abstract Construction of cytogenetic maps can provide important information for chromosome identification, chromosome evolution and genomic research. However, it hasn’t been conducted in many scallop species yet. In the present study, we attempted to map 12 fosmid clones containing tandem repeats by fluorescence in situ hybridization (FISH) in the Yesso scallop Patinopecten yessoensis (Jay, 1857). The results showed 6 fosmid clones were successfully mapped and distributed in 6 different pairs of chromosomes. Three clones were respectively assigned to a pair of metacentric chromosomes, a pair of submetacentric chromosomes and a pair of telocentric chromosomes and the remaining 3 clones showed their loci on three different pairs of subtelocentric chromosomes by co-hybridization. In summary, totally 8 pairs of chromosomes of the Yesso scallop were identified by 6 fosmid clones and two rDNA probes. Furthermore, 6 tandem repeats of 5 clones were sequenced and could be developed as chromosome specific markers for the Yesso scallop. The successful localization of fosmid clones will undoubtedly facilitate the integration of linkage groups with cytogenetic map and genomic research for the Yesso scallop. PMID:27186345

  16. Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM).

    PubMed

    Gosselin, Pauline; Rando, Gianpaolo; Fleury-Olela, Fabienne; Schibler, Ueli

    2016-08-15

    The discovery of transcription factors (TFs) controlling pathways in health and disease is of paramount interest. We designed a widely applicable method, dubbed barcorded synthetic tandem repeat promoter screening (BC-STAR-PROM), to identify signal-activated TFs without any a priori knowledge about their properties. The BC-STAR-PROM library consists of ∼3000 luciferase expression vectors, each harboring a promoter (composed of six tandem repeats of synthetic random DNA) and an associated barcode of 20 base pairs (bp) within the 3' untranslated mRNA region. Together, the promoter sequences encompass >400,000 bp of random DNA, a sequence complexity sufficient to capture most TFs. Cells transfected with the library are exposed to a signal, and the mRNAs that it encodes are counted by next-generation sequencing of the barcodes. This allows the simultaneous activity tracking of each of the ∼3000 synthetic promoters in a single experiment. Here we establish proof of concept for BC-STAR-PROM by applying it to the identification of TFs induced by drugs affecting actin and tubulin cytoskeleton dynamics. BC-STAR-PROM revealed that serum response factor (SRF) is the only immediate early TF induced by both actin polymerization and microtubule depolymerization. Such changes in cytoskeleton dynamics are known to occur during the cell division cycle, and real-time bioluminescence microscopy indeed revealed cell-autonomous SRF-myocardin-related TF (MRTF) activity bouts in proliferating cells. PMID:27601530

  17. The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats.

    PubMed

    Shen, Xin; Wang, Haiqing; Wang, Minxiao; Liu, Bin

    2011-11-01

    Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. Euphausia pacifica (Malacostraca: Euphausiacea) is one of the most important and dominant crustaceans in the North Pacific Ocean. In this paper, we described the gene content, organization, and codon usage of the E. pacifica mitochondrial genome. The mitochondrial genome of E. pacifica is 16 898 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Translocation of three transfer RNAs (trnL(1), trnL(2), and trnW) was found in the E. pacifica mitochondrial genome when comparing with the pancrustacean ground pattern. The rate of K(a)/K(s) in 13 protein-coding genes among three krill is much less than 1, which indicates a strong purifying selection within this group. The largest noncoding region in the E. pacifica mitochondrial genome contains one section with tandem repeats (4.7 x 154 bp), which are the largest tandem repeats found in malacostracan mitochondrial genomes so far. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, Brachyura, and Euphausiacea. The Bayesian analysis of nucleotide and amino acid datasets strongly supports the close relationship between Euphausiacea and Decapoda, which confirms traditional findings. The maximum likelihood analysis based on amino acid data strongly supports the close relationship between Euphausiacea and Penaeidae, which destroys the monophyly of Decapoda. PMID:22017501

  18. Inferring short tandem repeat variation from paired-end short reads

    PubMed Central

    Cao, Minh Duc; Tasker, Edward; Willadsen, Kai; Imelfort, Michael; Vishwanathan, Sailaja; Sureshkumar, Sridevi; Balasubramanian, Sureshkumar; Bodén, Mikael

    2014-01-01

    The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method’s ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats. PMID:24353318

  19. Sequence-based definition of eight short tandem repeat loci located within the HLA-region in an Austrian population.

    PubMed

    Dauber, Eva-Maria; Wenda, Sabine; Schwartz-Jungl, Elisabeth Maria; Glock, Barbara; Mayr, Wolfgang R

    2015-01-01

    Sequenced allelic ladders are a prerequisite for reliable genotyping of short tandem repeat (STR) polymorphisms and consistent results across instrument platforms. For eight STR-loci located on the short arm of chromosome 6 (6p21.3), a sequenced based nomenclature was established according to international recommendations. Publicly available reference DNA samples were sequenced enabling interested laboratories to construct their own allelic ladders. Three tetrameric (D6S2691, D6S2678, DQIV), one trimeric (D6S2906) and four dimeric repeat loci (D6S2972, D6S2792, D6S2789, D6S273) were investigated. Apart from the very complex sequence structure at the DQIV locus, three loci showed a compound and four loci a simple repeat pattern. In the flanking regions of some loci additional single nucleotide and insertion/deletion polymorphisms occurred as well as sequence polymorphisms within the repeat region of alleles with the same length. In an Austrian Caucasoid population sample (n=293) between eight and 22 alleles were found. No significant deviation from Hardy-Weinberg expectations was observed, the power of discrimination ranged from 0.826 to 0.978. The loci cover the HLA-coding region from HLA-A to HLA-DQB1 and can be used for a better definition of HLA haplotypes for population and disease association studies, recombination point mapping, haematopoietic stem cell transplantation as well as for identity and relationship testing. PMID:25450788

  20. Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe's oldest Camellia japonica.

    PubMed

    Heitkam, Tony; Petrasch, Stefan; Zakrzewski, Falk; Kögler, Anja; Wenke, Torsten; Wanke, Stefan; Schmidt, Thomas

    2015-12-01

    Northern Europe's oldest and largest Camellia japonica growing at the Pillnitz Castle (Germany) for over 200 years is of botanical and cultural importance and is a reference for C. japonica molecular scale analysis. In order to provide a fundament for genome analysis of the genus Camellia, we characterize the C. japonica tandem repeat fraction, constituting 12.5 % of the Pillnitz camellia's genome. A genomic library of the Pillnitz C. japonica was produced and Illumina sequenced to generate 36 Gb of paired-end reads. We performed graph-based read clustering implemented in the RepeatExplorer pipeline to estimate the C. japonica repeat fraction of 73 %. This enabled us to identify and characterize the most prominent satellite DNAs, Camellia japonica satellite 1-4 (CajaSat1-CajaSat4), and the 5S ribosomal DNA (rDNA) by bioinformatics, fluorescent in situ and Southern hybridization. Within the Camellia genus, satellite spreading, array expansion and formation of higher-order structures highlight different modes of repeat evolution. The CajaSat satellites localize at prominent chromosomal sites, including (peri)centromeres and subtelomeres of all chromosomes, thus serving as chromosomal landmarks for their identification. This work provides an insight into the C. japonica chromosome organization and significantly expands the Camellia genomic knowledge, also with respect to the tea plant Camellia sinensis. PMID:26582634

  1. Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin

    SciTech Connect

    Kusunoki, H.; Minasov, G.; Macdonald, R.I.; Mondragon, A.

    2010-03-08

    Previous X-ray crystal structures have shown that linkers of five amino acid residues connecting pairs of chicken brain {alpha}-spectrin and human erythroid {beta}-spectrin repeats can undergo bending without losing their {alpha}-helical structure. To test whether bending at one linker can influence bending at an adjacent linker, the structures of two and three repeat fragments of chicken brain {alpha}-spectrin have been determined by X-ray crystallography. The structure of the three-repeat fragment clearly shows that bending at one linker can occur independently of bending at an adjacent linker. This observation increases the possible trajectories of modeled chains of spectrin repeats. Furthermore, the three-repeat molecule crystallized as an antiparallel dimer with a significantly smaller buried interfacial area than that of {alpha}-actinin, a spectrin-related molecule, but large enough and of a type indicating biological specificity. Comparison of the structures of the spectrin and {alpha}-actinin dimers supports weak association of the former, which could not be detected by analytical ultracentrifugation, versus strong association of the latter, which has been observed by others. To correlate features of the structure with solution properties and to test a previous model of stable spectrin and dystrophin repeats, the number of inter-helical interactions in each repeat of several spectrin structures were counted and compared to their thermal stabilities. Inter-helical interactions, but not all interactions, increased in parallel with measured thermal stabilities of each repeat and in agreement with the thermal stabilities of two and three repeats and also partial repeats of spectrin.

  2. Chelating resin-based extraction of DNA from dental pulp and sex determination from incinerated teeth with Y-chromosomal alphoid repeat and short tandem repeats.

    PubMed

    Tsuchimochi, Tsukasa; Iwasa, Mineo; Maeno, Yoshitaka; Koyama, Hiroyoshi; Inoue, Hiroyuki; Isobe, Ichiro; Matoba, Ryoji; Yokoi, Motoo; Nagao, Masataka

    2002-09-01

    A procedure utilizing Chelex 100, chelating resin, was adapted to extract DNA from dental pulp. The procedure was simple and rapid, involved no organic solvents, and did not require multiple tube transfers. The extraction of DNA from dental pulp using this method was as efficient, or more so, than using proteinase K and phenol-chloroform extraction. In this study, the Chelex method was used with amplification and typing at Y-chromosomal loci to determine the effects of temperature on the sex determination of the teeth. The extracted teeth were incinerated in a dental furnace for 2 minutes at 100 degrees C, 200 degrees C, 300 degrees C, 400 degrees C, and 500 degrees C. After the isolation of DNA from the dental pulp by the Chelex method, alphoid repeats, and short tandem repeats, the human Y chromosome (DYZ3), DYS19, SYS389, DYS390, and DYS393 could be amplified and typed in all samples incinerated at up to 300 degrees C for 2 minutes. The DYS389 locus in some samples could not be amplified at 300 degrees C for 2 minutes. An autopsy case is described in which genotypings of DYS19, DYS390, and DYS393 from dental pulp obtained from a burned body were needed. The data presented in this report suggest that Chelex 100-based DNA extraction, amplification, and typing are possible in burned teeth in forensic autopsy cases. PMID:12198355

  3. Gene conversion plays the major role in controlling the stability of large tandem repeats in yeast.

    PubMed Central

    Gangloff, S; Zou, H; Rothstein, R

    1996-01-01

    The genomic stability of the rDNA tandem array in yeast is tightly controlled to allow sequence homogenization and at the same time prevent deleterious rearrangements. In our study, we show that gene conversion, and not unequal sister chromatid exchange, is the predominant recombination mechanism regulating the expansion and contraction of the rDNA array. Furthermore, we found that RAD52, which is essential for gene conversion, is required for marker duplication stimulated in the absence of the two yeast type I topoisomerases. Our results have implications for the mechanisms regulating genomic stability of repetitive sequence families found in all eukaryotes. Images PMID:8612596

  4. ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae

    PubMed Central

    2012-01-01

    Background Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. Results ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. Conclusions We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the

  5. Typing and Subtyping of Clostridium difficile Isolates by Using Multiple-Locus Variable-Number Tandem-Repeat Analysis▿

    PubMed Central

    van den Berg, Renate J.; Schaap, Inge; Templeton, Kate E.; Klaassen, Corné H. W.; Kuijper, Ed J.

    2007-01-01

    Using the genomic sequence of Clostridium difficile strain 630, we developed multiple-locus variable-number tandem-repeat analysis (MLVA) with automated fragment analysis and multicolored capillary electrophoresis as a typing method for C. difficile. All reference strains, representing 31 serogroups, 25 toxinotypes, and 7 known subtypes of PCR ribotype 001, could be discriminated from each other. Application of MLVA to 28 isolates from 7 outbreaks due to the emerging hypervirulent PCR ribotype 027-pulsed-field gel electrophoresis type NAP1 resulted in recognition of 13 clusters. Additionally, 29 toxin A-negative, toxin B-positive isolates belonging to PCR ribotype 017 from eight different countries revealed eight country-specific clusters. MLVA is a highly discriminatory genotyping method and a new tool for subtyping of newly emerging variants of C. difficile. PMID:17166961

  6. Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for the Molecular Subtyping of Enterobacter sakazakii▿

    PubMed Central

    Mullane, N. R.; Ryan, M.; Iversen, C.; Murphy, M.; O'Gaora, P.; Quinn, T.; Whyte, P.; Wall, P. G.; Fanning, S.

    2008-01-01

    The genomic content of Enterobacter sakazakii strain ATCC BAA-894 was analyzed for variable-number tandem repeats (VNTRs). In this study we report the development of a multiple-locus VNTR analysis (MLVA) strategy for the subtyping of E. sakazakii. The method is based on a GeneScan analysis of four VNTR loci labeled with multiple fluorescent dyes. This approach was applied to a collection of 112 isolates representing all 16 of the currently defined E. sakazakii biogroups. MLVA successfully discriminated among these isolates and compared favorably with pulsed-field gel electrophoresis. The method was relatively fast and easy to perform. The potential value of MLVA as an epidemiological tool is discussed. PMID:18083860

  7. A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

    PubMed Central

    Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

    2011-01-01

    Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10-17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

  8. Detection of a novel X-chromosomal short tandem repeat marker in Xq28 in four ethnic groups.

    PubMed

    Nishi, Takeki; Nakamura, Takako; Honda, Katuya

    2016-03-01

    DNA testing of X-chromosomal short tandem repeat (X-STR) polymorphisms has been the focus of attention in several studies, mainly due to its applicability in the investigation of complex kinship cases. Studies of X-STR in analyses of DNA sequences, population studies and DNA testing applications have been reported. We performed detection and population genetic study of a novel tetranucleotide X-STR locus in the present study. We identified a unique X-STR locus consisting of two tetranucleotides in Xq28. Although the STR is a simple tetranucleotide, its polymorphism was comparatively high [polymorphism information content (PIC)=0.7140] in Japanese subjects. In addition, the STR varied in structure among ethnic groups. We conclude that this locus will be useful for forensic DNA testing and anthropological studies. PMID:26980253

  9. Genetic Diversity of the Indian Populations of 'Candidatus Liberibacter asiaticus' Based on the Tandem Repeat Variability in a Genomic Locus.

    PubMed

    Ghosh, Dilip Kumar; Bhose, Sumit; Motghare, Manali; Warghane, Ashish; Mukherjee, Krishanu; Ghosh, Dipak Kumar; Sharma, Ashwani Kumar; Ladaniya, Milind Shivratan; Gowda, Siddarame

    2015-08-01

    Citrus huanglongbing (HLB, citrus greening disease) is an extremely destructive disease affecting citrus and causes severe economic loss to the crop yield worldwide. The disease is caused by a phloem-limited, noncultured, gram-negative bacteria Candidatus Liberibacter spp., the widely present and most destructive species being 'Candidatus Liberibacter asiaticus'. Although the disease has been reported from almost all citrus growing regions of India, knowledge on the molecular variability of the pathogen 'Ca. L. asiaticus' populations from different geographical regions and cultivars is limited. In the present study, variability of the Indian 'Ca. L. asiaticus' based on the tandem repeats at the genomic locus CLIBASIA_01645 was characterized and categorized into four classes based on the tandem repeat number (TRN); Class I (TRN≤5), Class II (TRN>5≤10), Class III (TRN>10≤15), and Class IV (TRN>15). The study revealed that the Indian population of 'Ca. L. asiaticus' is more diverse than reported for Florida and Guangdong populations, which showed less diversity. While Florida and Guangdong populations were dominated by a TRN5 and TRN7 genotype, respectively, the Indian 'Ca. L. asiaticus' populations with TRN copy numbers 9, 10, 11, 12, and 13 were widely distributed throughout the country. Additionally, TRN2 and TRN17 genotypes were also observed among the Indian 'Ca. L. asiaticus' populations. The predominant 'Ca. L. asiaticus' genotypes from the northeastern region of India were TRN6 and TRN7 (53.12%) and surprisingly similar to neighboring South China populations. Preliminary results showed absence of preference of citrus cultivars to any specific 'Ca. L. asiaticus' genotype. PMID:25760522

  10. Macromolecular organization and genetic mapping of a rapidly evolving chromosome-specific tandem repeat family (B77) in cotton (Gossypium).

    PubMed

    Zhao, X; Ji, Y; Ding, X; Stelly, D M; Paterson, A H

    1998-12-01

    Isolation and characterization of the most prominent repetitive element families in the genome of tetraploid cotton (Gossypium barbadense L; [39]) revealed a small subset of families that showed very different properties in tetraploids than in their diploid progenitors, separated by 1-2 million years. One element, B77, was characterized in detail, and compared to the well-conserved 5S and 45S rRNA genes. The 572 bp B77 repeat was found to be concentrated in several discontinuous tandem arrays confined to a single 550 kb SalI fragment in tetraploid cotton. Genetic mapping based on the absence of the pentameric 'rung' in the G. barbadense 'ladder' showed that B77 maps to a D-subgenome chromosome. In situ hybridization supports the contention that the array is confined largely to a single chromosomal site in the D-subgenome. The B77 repeat has undergone a substantial increase in copy number since formation of tetraploid cotton from its diploid relatives. RFLPs observed among tetraploid cotton species suggest that amplification and/or rearrangement of the repeat may have continued after divergence of the five tetraploid cotton species. B77 contains many short direct repeats and shares significant DNA sequence homology with a Nicotiana alata retrotransposon Tna1-2 integrase motif. The recent amplification of B77 on linkage group D04 suggests that the D-subgenome of tetraploid cotton may be subject to different evolutionary constraints than the D-genome diploid chromosomes, which exhibit few genome-specific elements. Further, the abundance of B77 in G. gossypioides supports independent evidence that it may be the closest extant relative of the D-genome ancestor of cotton. PMID:9869409

  11. Tri-allelic pattern of short tandem repeats identifies the murderer among identical twins and suggests an embryonic mutational origin.

    PubMed

    Wang, Li-Feng; Yang, Ying; Zhang, Xiao-Nan; Quan, Xiao-Liang; Wu, Yuan-Ming

    2015-05-01

    Monozygotic twins can be co-identified by genotyping of short tandem repeats (STRs); however, for distinguishing them, STR genotyping is ineffective, especially in the case of murder. Here, a rarely occurring tri-allelic pattern in the vWA locus (16, 18, 19) was identified only in the DNA of one identical twin, which could help to exonerate the innocent twin in a murder charge. This mutation was defined as primary through genotyping of the family and could be detected in blood, buccal and semen samples from the individual; however, two alternative allele-balanced di-allelic patterns (16, 18 or 16, 19) were detected in hair root sheath cells. Such a kind of segregation indicates a one-step mutation occurs in cell mitosis, which is after embryonic zygote formation and during the early development of the individual after the division of the blastocyte. Sequencing revealed the insertion between the allele 18 and 19 is a repeat unit of TAGA/TCTA (plus/minus strand), which belongs to "AGAT/ATCT"-based core repeats identified from all tri-allelic pattern reports recorded in the STR base and a detailed model was proposed for STR repeat length variation caused by false priming during DNA synthesis. Our model illustrates the possible origination of allele-balanced and unbalanced tri-allelic pattern, clarifies that the genotypes of parent-child mismatches, aberrant di-allelic patterns, and type 1 or 2 tri-allelic patterns should be considered as independent, but interconnected forms of STR mutation. PMID:25732248

  12. Characterization of Dutch Staphylococcus aureus from bovine mastitis using a Multiple Locus Variable Number Tandem Repeat Analysis.

    PubMed

    Ikawaty, Risma; Brouwer, E C; Jansen, M D; van Duijkeren, E; Mevius, D; Verhoef, J; Fluit, A C

    2009-05-12

    Current typing methods for Staphylococcus aureus have important drawbacks. We evaluated a Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) scheme with 6 loci which lacks most drawbacks on 85 bovine mastitis isolates from The Netherlands. For each locus the number of repeat units (RU) was calculated. Each combination of repeat units was assigned a MLVA-type (MT). We compared the MLVA typing result with Multi Locus Sequence Typing (MLST), spa-typing and Pulsed-Field Gel Electrophoresis (PFGE). MLVA typing resulted in 18 MTs, although 3 loci could not always be amplified. Spa-typing distinguished 10 spa-types including 3 dominant and 2 new types. PFGE showed 5 dominant profiles with 15 related profiles and 6 unique profiles. MLST showed 4 dominant STs. Some types appeared to be bovine specific. The Simpson's Indices of diversity for PFGE, MLST, spa-typing and MLVA were 0.887, 0.831, 0.69 and 0.781, respectively, indicating that discriminatory power of MLVA was between MLST and spa-typing, whereas PFGE displayed the highest discriminatory power. However, MLVA is fast and cheap when compared to the other methods. The Adjusted Rand index and Wallace's coefficient indicated that MLVA was highly predictive for spa-type, but not vice versa. Analysis of the region neighboring SIRU05 showed a difference in the genetic element bordering the repeats of SIRU05 that explained the negative SIRU05 PCRs. PFGE, MLST, and MLVA are adequate typing methods for bovine-associated S. aureus. PMID:19101101

  13. 5meCpG Epigenetic Marks Neighboring a Primate-Conserved Core Promoter Short Tandem Repeat Indicate X-Chromosome Inactivation

    PubMed Central

    Machado, Filipe Brum; Machado, Fabricio Brum; Faria, Milena Amendro; Lovatel, Viviane Lamim; Alves da Silva, Antonio Francisco; Radic, Claudia Pamela; De Brasi, Carlos Daniel; Rios, Álvaro Fabricio Lopes; de Sousa Lopes, Susana Marina Chuva; da Silveira, Leonardo Serafim; Ruiz-Miranda, Carlos Ramon; Ramos, Ester Silveira; Medina-Acosta, Enrique

    2014-01-01

    X-chromosome inactivation (XCI) is the epigenetic transcriptional silencing of an X-chromosome during the early stages of embryonic development in female eutherian mammals. XCI assures monoallelic expression in each cell and compensation for dosage-sensitive X-linked genes between females (XX) and males (XY). DNA methylation at the carbon-5 position of the cytosine pyrimidine ring in the context of a CpG dinucleotide sequence (5meCpG) in promoter regions is a key epigenetic marker for transcriptional gene silencing. Using computational analysis, we revealed an extragenic tandem GAAA repeat 230-bp from the landmark CpG island of the human X-linked retinitis pigmentosa 2 RP2 promoter whose 5meCpG status correlates with XCI. We used this RP2 onshore tandem GAAA repeat to develop an allele-specific 5meCpG-based PCR assay that is highly concordant with the human androgen receptor (AR) exonic tandem CAG repeat-based standard HUMARA assay in discriminating active (Xa) from inactive (Xi) X-chromosomes. The RP2 onshore tandem GAAA repeat contains neutral features that are lacking in the AR disease-linked tandem CAG repeat, is highly polymorphic (heterozygosity rates approximately 0.8) and shows minimal variation in the Xa/Xi ratio. The combined informativeness of RP2/AR is approximately 0.97, and this assay excels at determining the 5meCpG status of alleles at the Xp (RP2) and Xq (AR) chromosome arms in a single reaction. These findings are relevant and directly translatable to nonhuman primate models of XCI in which the AR CAG-repeat is monomorphic. We conducted the RP2 onshore tandem GAAA repeat assay in the naturally occurring chimeric New World monkey marmoset (Callitrichidae) and found it to be informative. The RP2 onshore tandem GAAA repeat will facilitate studies on the variable phenotypic expression of dominant and recessive X-linked diseases, epigenetic changes in twins, the physiology of aging hematopoiesis, the pathogenesis of age-related hematopoietic

  14. First isolation of tandemly repeated DNA sequences in New World vultures and phylogenetic implications.

    PubMed

    Keyser, C; Montagnon, D; Schlee, M; Ludes, B; Pfitzinger, H; Mangin, P

    1996-02-01

    A highly repeated DNA sequence composed of closely related subunits that ranged from 171 to 176 base pairs has been cloned and characterized in the king vulture (Sarcoramphus papa). Related sequences were also isolated in the black vulture (Coragyps atratus). This new family of avian repetitive DNA elements is here termed the "HaeIII family." Genomic DNAs from a number of avian species were probed with one of the king vulture restriction fragments. In the cathartids, the hybridization patterns showed no individual or sexual variations. A strong HaeIII ladder was present in the two aforementioned species as well as in the Andean condor (Vultur gryphus), but in the black vulture the bands of the ladder alternated in intensity. Weaker hybridization signals were obtained in two ciconids, the jabiru stork (Jabiru mycteria) and the white stork (Ciconia ciconia). The HaeIII repeat was not detected in accipitrid birds of prey, a Polyborinae falconid, pelecanids, and psittacids. PMID:8851796

  15. Mutation rates at Y chromosome short tandem repeats in Texas populations.

    PubMed

    Ge, Jianye; Budowle, Bruce; Aranda, Xavier G; Planz, John V; Eisenberg, Arthur J; Chakraborty, Ranajit

    2009-06-01

    Father-son pairs from three populations (African American, Caucasian, and Hispanic) of Texas were typed for the 17 Y STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR YfilerTM kit. With 49,578 allele transfers, 102 mutations were detected. One three-step and four two-step mutations were found, and all others (95.1%) were one-step mutations. The number of gains (48) and losses (54) of repeats were nearly similar. The average mutation rate in the total population is 2.1 x 10(-3) per locus (95% CI (1.7-2.5)x10(-3)). African Americans showed a higher mutation rate (3.0 x 10(-3); 95% CI (2.4-4.0)x10(-3)) than the Caucasians (1.7 x 10(-3); 95% CI (1.1-2.5)x10(-3)) and Hispanics (1.5 x 10(-3); 95% CI (1.0-2.2)x10(-3)), but grouped by repeat-lengths, such differences were not significant. Mutation is correlated with relative length of alleles, i.e., longer alleles are more likely to mutate compared with the shorter ones at the same locus. Mutation rates are also correlated with the absolute number of repeats, namely, alleles with higher number of repeats are more likely to mutate than the shorter ones (p-value=0.030). Finally, occurrences of none, one, and two mutations over the father-son transmission of alleles were consistent with the assumption of independence of mutation rates across loci. PMID:19414166

  16. Rapid sizing of short tandem repeat alleles using capillary array electrophoresis and energy-transfer fluorescent primers

    SciTech Connect

    Wang, Y.; Ju, J.; Carpenter, B.A.; Atherton, J.M.; Sensabaugh, G.F.; Mathies, R.A.

    1995-04-01

    Genetic typing of the short tandem repeat (STR) polymorphism HUMTHO1 has been performed using capillary array electroporesis and energy-transfer fluorescent dye-labeled polymerase chain reaction primers. Target alleles were amplified by use of primers labeled with one fluorescein at the 5` end and another fluorescein at the position of the 15th (modified) base to produce fragments that fluoresce in the green ({lambda}{sub max} = 525 nm). Unknown alleles were electrophoretically separated together with a standard ladder made up of alleles having 6, 7, 8, and 9 four-base pair repeats, each of which was amplified with an energy-transfer primer having a donor fluorescein at the 5` end and a rhodamine acceptor at the position of the 7th (modified) base to produce standard fragments fluorescing in the red (>590 nm). Separations are complete in less than 20 min and allow sizing with an absolute error or accuracy of less than 0.4 base pair and an average standard deviation of nearly 0.5 base pair with no correction for mobility shift and cross-talk between the fluorescence channels. This work establishes feasibility of high-speed, high-throughput STR typing of double-stranded DNA fragments using capillary array electrophoresis. 27 refs., 7 figs., 1 tab.

  17. A Tandem Repeat in Decay Accelerating Factor 1 Is Associated with Severity of Murine Mercury-Induced Autoimmunity

    PubMed Central

    Gabriel, Rodney; Kono, Dwight H.; Hultman, Per; Pollard, K. Michael

    2014-01-01

    Decay accelerating factor (DAF), a complement-regulatory protein, protects cells from bystander complement-mediated lysis and negatively regulates T cells. Reduced expression of DAF occurs in several systemic autoimmune diseases including systemic lupus erythematosus, and DAF deficiency exacerbates disease in several autoimmune models, including murine mercury-induced autoimmunity (mHgIA). Daf1, located within Hmr1, a chromosome 1 locus associated in DBA/2 mice with resistance to mHgIA, could be a candidate. Here we show that reduced Daf1 transcription in lupus-prone mice was not associated with a reduction in the Daf1 transcription factor SP1. Studies of NZB mice congenic for the mHgIA-resistant DBA/2 Hmr1 locus suggested that Daf1 expression was controlled by the host genome and not the Hmr1 locus. A unique pentanucleotide repeat variant in the second intron of Daf1 in DBA/2 mice was identified and shown in F2 intercrosses to be associated with less severe disease; however, analysis of Hmr1 congenics indicated that this most likely reflected the presence of autoimmunity-predisposing genetic variants within the Hmr1 locus or that Daf1 expression is mediated by the tandem repeat in epistasis with other genetic variants present in autoimmune-prone mice. These studies argue that the effect of DAF on autoimmunity is complex and may require multiple genetic elements. PMID:24818014

  18. Tandem repeat of a seven-bladed beta-propeller domain in oligoxyloglucan reducing-end-specific cellobiohydrolase.

    PubMed

    Yaoi, Katsuro; Kondo, Hidemasa; Noro, Natsuko; Suzuki, Mamoru; Tsuda, Sakae; Mitsuishi, Yasushi

    2004-07-01

    Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH; EC 3.2.1.150) is an exoglucanase that recognizes the reducing end of oligoxyloglucan and releases two glucosyl residue segments from the main chain. The X-ray crystal structure of OXG-RCBH determined at 2.2 A resolution reveals a unique feature of this enzyme; OXG-RCBH consists of a tandem repeat of two similar domains, which are both folded into seven-bladed beta-propeller structures. The sequence alignment of the propeller blades, based on the structure, indicates that a weak repeat of the amino acid sequence occurred seven times to construct each domain. There is a cleft that can accommodate the substrate oligosaccharide between the two domains, which is a putative substrate binding subsite. Mutation of either Asp35 or Asp465, located in the putative catalytic center, to Asn resulted in a protein with no detectable catalytic activity, indicating the critical role of these amino acids in catalysis. PMID:15242597

  19. Characterisation of novel and rare Y-chromosome short tandem repeat alleles in self-declared South Australian Aboriginal database.

    PubMed

    Collins, Tegan E; Ottens, Renee; Ballantyne, Kaye N; Nagle, Nano; Henry, Julianne; Taylor, Duncan; Gardner, Michael G; Fitch, Alison J; Goodman, Amanda; van Oorschot, Roland A H; Mitchell, R John; Linacre, Adrian

    2014-01-01

    Y-chromosome short tandem repeats (Y-STRs) are used in forensic science laboratories all over the world, as their application is wide and often vital in solving casework. Analysis of an in-house database of South Australian self-declared Aboriginal males held by Forensic Science South Australia (FSSA) using the Applied Biosystem's AmpFℓSTR® Yfiler™ PCR Amplification Kit revealed 43 variant Y-STR alleles at 6 of the 17 loci. All variant alleles were sequenced to determine the exact repeat structure for each. As a high level of admixture has previously been found within the SA Aboriginal database, samples were haplogrouped using Y-SNPs to determine their likely geographical origin. Although a number of variant alleles were associated with non-Aboriginal Y-haplogroups, a high frequency was observed within the Australian K-M9 lineage. Detailed knowledge of these variant alleles may have further application in the development of new DNA markers for identification purposes, and in population and evolutionary studies of Australian Aborigines. PMID:24048501

  20. Limitations of Spoligotyping and Variable-Number Tandem-Repeat Typing for Molecular Tracing of Mycobacterium bovis in a High-Diversity Setting▿ †

    PubMed Central

    Rodriguez-Campos, Sabrina; Aranaz, Alicia; de Juan, Lucía; Sáez-Llorente, José Luis; Romero, Beatriz; Bezos, Javier; Jiménez, Antonio; Mateos, Ana; Domínguez, Lucas

    2011-01-01

    This study describes the attempt to trace the first Mycobacterium bovis outbreak in alpacas (Lama pacos) in Spain by spoligotyping and variable-number tandem-repeat (VNTR) analysis. Due to high genotype diversity, no matching source was identified, but local expansion of a clonal group was found and its significance for molecular tracing is discussed. PMID:21752973

  1. Whole genome evaluation of tandem repeat polymorphisms between two pathogenically similar strains of Xylella fastidiosa isolated from almond and grape in California

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole genome tandem repeat polymorphisms were evaluated between two closely related Xylella fastidiosa strains, M23 and Temecula1, both cause almond leaf scorch disease (ALSD) and grape Pierce’s disease (PD) in California. Strain M23 was isolated from almond and the genome was sequenced in this stu...

  2. Multiplex Amplified Nominal Tandem-Repeat Analysis (MANTRA), a Rapid Method for Genotyping Mycobacterium tuberculosis by Use of Multiplex PCR and a Microfluidic Laboratory Chip ▿

    PubMed Central

    Merritt, Adam J.; Keehner, Terillee; O'Reilly, Lyn C.; McInnes, Russell L.; Inglis, Timothy J. J.

    2010-01-01

    A variable-number tandem-repeat genotyping method for Mycobacterium tuberculosis was converted to run in a multiplex PCR format on a 12-well microfluidic laboratory chip. Epidemiologically and genotypically distinct isolate clusters of M. tuberculosis were identified. This rapid genotyping method has potential application in smaller clinical laboratories and public health field investigations. PMID:20702663

  3. Enhanced immunogenicity of peptide P277 by heat shock protein HSP65 vector carrying tandem repeats of P277 to prevent type 1 diabetes in NOD mice.

    PubMed

    Liang, J; Aihua, Z; Yu, W; Jingjing, L

    2008-10-01

    The peptide P277 contains a target epitope for diabetogenic T cells and it has been used as an ideal target antigen to develop vaccines against type 1 diabetes. A major problem in developing P277 vaccine is its low immunogenicity. Recent applications involving multiple copies of self-peptide in linear alignment and conjugation with carrier proteins appear to increase the immune response. In this study, we designed a method based on isocaudamer technique to repeat tandemly the 24-residue sequence P277, then 6 tandemly repeated copies of the peptide P277 were fused to mycobacterial heat-shock protein 65 to construct a fusion protein HSP65-6xP277 as an immunogen. We examined the effect of the tandem repeats of the peptide P277 in eliciting an immune response by comparing the immunogenicity of the three immunogens: P277, HSP65-P277 and HSP65-6xP277. Immunization of mice with the fusion protein HSP65-6xP277 elicited much higher levels of specific anti-P277 antibodies than with P277 and HSP65-P277, which should suggest that multiple tandem repeats of a certain epitope is an efficient method to overcome the low immunogenicity of self-peptide antigens and the immunogen HSP65-6xP277 might be further developed to a vaccine against type 1 diabetes. PMID:18473288

  4. Structural Insights into the Cooperative Binding of SeqA to a Tandem GATC Repeat

    SciTech Connect

    Chung, Y.; Brendler, T; Austin, S; Guarne, A

    2009-01-01

    SeqA is a negative regulator of DNA replication in Escherichia coli and related bacteria that functions by sequestering the origin of replication and facilitating its resetting after every initiation event. Inactivation of the seqA gene leads to unsynchronized rounds of replication, abnormal localization of nucleoids and increased negative superhelicity. Excess SeqA also disrupts replication synchrony and affects cell division. SeqA exerts its functions by binding clusters of transiently hemimethylated GATC sequences generated during replication. However, the molecular mechanisms that trigger formation and disassembly of such complex are unclear. We present here the crystal structure of a dimeric mutant of SeqA [SeqA{Delta}(41-59)-A25R] bound to tandem hemimethylated GATC sites. The structure delineates how SeqA forms a high-affinity complex with DNA and it suggests why SeqA only recognizes GATC sites at certain spacings. The SeqA-DNA complex also unveils additional protein-protein interaction surfaces that mediate the formation of higher ordered complexes upon binding to newly replicated DNA. Based on this data, we propose a model describing how SeqA interacts with newly replicated DNA within the origin of replication and at the replication forks.

  5. Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

    PubMed Central

    Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

    2014-01-01

    Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community. PMID:25148383

  6. Determination of Sources of Escherichia coli on Beef by Multiple-Locus Variable-Number Tandem Repeat Analysis.

    PubMed

    Yang, Xianqin; Tran, Frances; Youssef, Mohamed K; Gill, Colin O

    2015-07-01

    The possible origin of Escherichia coli found on cuts and trimmings in the breaking facility of a beef packing plant was examined using multiple-locus variable-number tandem repeat analysis. Coliforms and E. coli were enumerated in samples obtained from 160 carcasses that would enter the breaking facility when work commenced and after each of the three production breaks throughout the day, from the conveyor belt before work and after each break, and from cuts and trimmings when work commenced and after each break. Most samples yielded no E. coli, irrespective of the surface types. E. coli was recovered from 7 (<5%) carcasses, at numbers mostly ≤1.0 log CFU/160,000 cm(2). The log total numbers of E. coli recovered from the conveyor belt, cuts, and trimmings were mostly between 1 and 2 log CFU/80,000 cm(2). A total of 554 E. coli isolates were recovered. Multiple-locus variable-number tandem repeat analysis of 327 selected isolates identified 80 distinct genotypes, with 37 (46%) each containing one isolate. However, 28% of the isolates were of genotypes that were recovered from more than one sampling day. Of the 80 genotypes, 65 and 2% were found in one or all four sampling periods throughout the day. However, they represented 23 and 14% of the isolates, respectively. Of the genotypes identified for each surface type, at least one contained ≥9 isolates. No unique genotypes were associated with carcasses, but 10, 17, and 19 were uniquely associated with cuts, trimmings, and the belt, respectively. Of the isolates recovered from cuts, 49, 3, and 19% were of genotypes that were found among isolates recovered from the belt, carcasses, or both the belt and carcasses, respectively. A similar composition was found for isolates recovered from trimmings. These findings show that the E. coli found on cuts and trimmings at this beef packing plant mainly originated from the conveyor belt and that small number of E. coli strains survived the daily cleaning and sanitation

  7. Molecular Typing of Mycobacterium intracellulare Using Pulsed-Field Gel Electrophoresis, Variable-Number Tandem-Repeat Analysis, Mycobacteria Interspersed Repetitive-Unit-Variable-Number Tandem Repeat Typing, and Multilocus Sequence Typing: Molecular Characterization and Comparison of Each Typing Methods

    PubMed Central

    Jeon, Semi; Lim, Nara; Kwon, Seungjik; Shim, Taesun; Park, Misun; Kim, Bum-Joon; Kim, Seonghan

    2014-01-01

    Objectives Mycobacterium intracellulare is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of M. intracellulare is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods. Methods Antibiotic susceptibility testing, hsp65 and rpoB sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria interspersed repetitive-unit-variable-number tandem-repeat analysis (MIRU-VNTR), and VNTR assay targeting 44 M. intracellulare isolates obtained from patients with pulmonary infections were performed. Results All the antibiotic susceptibility patterns had no association with the molecular and sequence types tested in this study; however, the molecular and sequence types were related with each other. PFGE gave best results for discriminatory capacity, followed by VNTR, MLST, and MIRU-VNTR. Conclusion The high discriminatory power of PFGE, VNTR, and MLST is enough for differentiating between reinfection and relapse, as well as for other molecular epidemiological usages. The MLST could be regarded as a representative classification method, because it showed the clearest relation with the sequence types. PMID:25180144

  8. Characterization of the uup locus and its role in transposon excisions and tandem repeat deletions in Escherichia coli.

    PubMed

    Reddy, M; Gowrishankar, J

    2000-04-01

    Null mutations in the Escherichia coli uup locus (at 21.8 min) serve to increase the frequency of RecA-independent precise excision of transposable elements such as Tn10 and to reduce the plaque size of bacteriophage Mu (Uup(-) phenotype). By the combined approaches of physical mapping of the mutations, complementation analyses, and protein overexpression from cloned gene fragments, we have demonstrated in this study that the Uup(-) phenotype is the consequence of the absence of expression of the downstream gene (uup) of a two-gene operon, caused either directly by insertions in uup or indirectly by the polar effect of insertions in the upstream gene (ycbY). The promoter for uup was mapped upstream of ycbY by primer extension analysis on cellular RNA, and assays of reporter gene expression indicated that it is a moderately active, constitutive promoter. The uup mutations were also shown to increase, in a RecA-independent manner, the frequencies of nearly precise excision of Tn10 derivatives and of the deletion of one copy of a chromosomal tandem repeat, suggesting the existence of a shared step or intermediate in the pathways of these latter events and that of precise excision. Finally, we found that mutations that increase the frequency of precise excision of Tn10 are divisible into two categories, depending upon whether they did (uup, ssb, polA, and topA) or did not (mutHLS, dam, and uvrD) also increase precise excision frequency of the mini-Tn10 derivatives. It is suggested that the differential response of mini-Tn10 and Tn10 to the second category of mutations is related to the presence, respectively, of perfect and of imperfect terminal inverted repeats in them. PMID:10715006

  9. A Systematic Evaluation of Short Tandem Repeats in Lipid Candidate Genes: Riding on the SNP-Wave

    PubMed Central

    Lamina, Claudia; Haun, Margot; Coassin, Stefan; Kloss-Brandstätter, Anita; Gieger, Christian; Peters, Annette; Grallert, Harald; Strauch, Konstantin; Meitinger, Thomas; Kedenko, Lyudmyla; Paulweber, Bernhard; Kronenberg, Florian

    2014-01-01

    Structural genetic variants as short tandem repeats (STRs) are not targeted in SNP-based association studies and thus, their possible association signals are missed. We systematically searched for STRs in gene regions known to contribute to total cholesterol, HDL cholesterol, LDL cholesterol and triglyceride levels in two independent studies (KORA F4, n = 2553 and SAPHIR, n = 1648), resulting in 16 STRs that were finally evaluated. In a combined dataset of both studies, the sum of STR alleles was regressed on each phenotype, adjusted for age and sex. The association analyses were repeated for SNPs in a 200 kb region surrounding the respective STRs in the KORA F4 Study. Three STRs were significantly associated with total cholesterol (within LDLR, the APOA1/C3/A4/A5/BUD13 gene region and ABCG5/8), five with HDL cholesterol (3 within CETP, one in LPL and one inAPOA1/C3/A4/A5/BUD13), three with LDL cholesterol (LDLR, ABCG5/8 and CETP) and two with triglycerides (APOA1/C3/A4/A5/BUD13 and LPL). None of the investigated STRs, however, showed a significant association after adjusting for the lead or adjacent SNPs within that gene region. The evaluated STRs were found to be well tagged by the lead SNP within the respective gene regions. Therefore, the STRs reflect the association signals based on surrounding SNPs. In conclusion, none of the STRs contributed additionally to the SNP-based association signals identified in GWAS on lipid traits. PMID:25050552

  10. Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats.

    PubMed

    Vera, Manuel; Bello, Xabier; Álvarez-Dios, Jose-Antonio; Pardo, Belen G; Sánchez, Laura; Carlsson, Jens; Carlsson, Jeanette E L; Bartolomé, Carolina; Maside, Xulio; Martinez, Paulino

    2015-12-01

    The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but its production has been greatly reduced by the parasite Bonamia ostreae. Here, new generation genomic resources were used to analyse the repetitive fraction of the oyster genome, with the aim of developing molecular markers to face this main oyster production challenge. The resulting oyster database, consists of two sets of 10,318 and 7159 unique contigs (4.8 Mbp and 6.8 Mbp in total length) representing the oyster's genome (WG) and haemocyte transcriptome (HT), respectively. A total of 1083 sequences were identified as TE-derived, which corresponded to 4.0% of WG and 1.1% of HT. They were clustered into 142 homology groups, most of which were assigned to the Penelope order of retrotransposons, and to the Helitron and TIR DNA-transposons. Simple repeats and rRNA pseudogenes, also made a significant contribution to the oyster's genome (0.5% and 0.3% of WG and HT, respectively).The most frequent short tandem repeats identified in WG were tetranucleotide motifs while trinucleotide motifs were in HT. Forty identified microsatellite loci, 20 from each database, were selected for technical validation. Success was much lower among WG than HT microsatellites (15% vs 55%), which could reflect higher variation in anonymous regions interfering with primer annealing. All microsatellites developed adjusted to Hardy-Weinberg proportions and represent a useful tool to support future breeding programmes and to manage genetic resources of natural flat oyster beds. PMID:26341181

  11. Identification and Characterization of Variable-Number Tandem-Repeat Markers for Typing of Brucella spp.†

    PubMed Central

    Whatmore, Adrian M.; Shankster, Stephen J.; Perrett, Lorraine L.; Murphy, Terry J.; Brew, Simon D.; Thirlwall, Rachel E.; Cutler, Sally J.; MacMillan, Alastair P.

    2006-01-01

    Members of the genus Brucella infect many domesticated and wild animals and cause serious zoonotic infection in humans. The availability of discriminatory molecular typing tools to inform and assist conventional epidemiological approaches would be invaluable in controlling these infections, but efforts have been hampered by the genetic homogeneity of the genus. We report here on a molecular subtyping system based on 21 variable-number tandem-repeat (VNTR) loci consisting of 13 previously unreported loci and 8 loci previously reported elsewhere. This approach was applied to a collection of 121 Brucella isolates obtained worldwide and representing all six classically recognized Brucella species. The size of repeats selected for inclusion varied from 5 to 40 bp giving VNTR loci with a range of diversities. The number of alleles detected ranged from 2 to 21, and Simpson's diversity index values ranged from 0.31 to 0.92. This assay divides the 121 isolates into 119 genotypes, and clustering analysis results in groups that, with minor exceptions, correspond to conventional species designations. Reflecting this, the use of six loci in isolation was shown to be sufficient to determine species designation. On the basis of the more variable loci, the assay could also discriminate isolates originating from restricted geographical sources, indicating its potential as an epidemiological tool. Stability studies carried out in vivo and in vitro showed that VNTR profiles were sufficiently stable such that recovered strains could readily be identified as the input strain. The method described here shows great potential for further development and application to both epidemiological tracing of Brucella transmissions and in determining relationships between isolates worldwide. PMID:16757588

  12. Von Willebrand gene tracking by single-tube automated fluorescent analysis of four short tandem repeat polymorphisms.

    PubMed

    Vidal, Francisco; Julià, Antoni; Altisent, Carme; Puig, Lluís; Gallardo, Doinique

    2005-05-01

    Molecular diagnosis of von Willebrand disease (VWD) has been hampered by the large size and complex genomic characteristics of the gene involved. For this reason, indirect methods using intragenic polymorphic markers described along the von Willebrand factor (VWF) gene are valuable tools for gene monitoring and linkage analysis. Several studies have demonstrated the four commonly utilized short tandem repeats (STRs), three located in intron 40 and one in the promoter region of the VWF gene, to be highly informative for this task. Our objective was t o develop a rapid, automated method to simultaneously analyze these four STRs for VWF gene tracking. Amplification of the four loci is achieved in a single multiplex fluorescent PCR which is then analyzed in the same run by capillary electrophoresis. Data processing with GeneScan and Genotyper software has simplified management and tabulation of the resulting haplotypes. Analysis of the VWF gene in DNA from 102 individuals (204 chromosomes) revealed that the three STRs within intron 40 showed significant linkage disequilibrium against each other but not against the VWP locus. Moreover, the combination of the four markers offers a high heterozygosity rate (>99%) that improves tracing VWF gene inheritance. In conclusion, the automated fluorescent capillary electrophoresis method presented here is an extremely rapid, simple and highly informative technique for association studies between VWD and the VWF gene in addition to genetic counseling and prenatal diagnosis by precise linkage analysis in VWD-affected families. PMID:15886817

  13. Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats

    PubMed Central

    Sapawi, Azizian Mohd; Salleh, Mohd Zaki

    2015-01-01

    Abstract Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering large-scale Y-STR data, represents a promising method for developing these tools. In this study we improved the k-AMH and produced three new algorithms: the Nk-AMH I (including a new initial cluster center selection), the Nk-AMH II (including a new dominant weighting value), and the Nk-AMH III (combining I and II). The Nk-AMH III was the superior algorithm, with mean clustering accuracy that increased in four out of six datasets and remained at 100% in the other two. Additionally, the Nk-AMH III achieved a 2% higher overall mean clustering accuracy score than the k-AMH, as well as optimal accuracy for all datasets (0.84–1.00). With inclusion of the two new methods, the Nk-AMH III produced an optimal solution for clustering Y-STR data; thus, the algorithm has potential for further development towards fully automatic clustering of any large-scale genotypic data. PMID:25945508

  14. Variant Alleles, Triallelic Patterns, and Point Mutations Observed in Nuclear Short Tandem Repeat Typing of Populations in Bosnia and Serbia

    PubMed Central

    Huel, René L. M.; Bašić, Lara; Madacki-Todorović, Kamelija; Smajlović, Lejla; Eminović, Izet; Berbić, Irfan; Miloš, Ana; Parsons, Thomas J.

    2007-01-01

    Aim To present a compendium of off-ladder alleles and other genotyping irregularities relating to rare/unexpected population genetic variation, observed in a large short tandem repeat (STR) database from Bosnia and Serbia. Methods DNA was extracted from blood stain cards relating to reference samples from a population of 32 800 individuals from Bosnia and Serbia, and typed using Promega’s PowerPlex®16 STR kit. Results There were 31 distinct off-ladder alleles were observed in 10 of the 15 STR loci amplified from the PowerPlex®16 STR kit. Of these 31 alleles, 3 have not been previously reported. Furthermore, 16 instances of triallelic patterns were observed in 9 of the 15 loci. Primer binding site mismatches that affected amplification were observed in two loci, D5S818 and D8S1179. Conclusion Instances of deviations from manufacturer’s allelic ladders should be expected and caution taken to properly designate the correct alleles in large DNA databases. Particular care should be taken in kinship matching or paternity cases as incorrect designation of any of these deviations from allelic ladders could lead to false exclusions. PMID:17696304

  15. Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant

    NASA Astrophysics Data System (ADS)

    Yuchi, Zhiguang; Yuen, Siobhan M. Wong King; Lau, Kelvin; Underhill, Ainsley Q.; Cornea, Razvan L.; Fessenden, James D.; van Petegem, Filip

    2015-08-01

    Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca2+-dependent signalling events, and consist of several globular domains that together form a large assembly. Here we describe the crystal structures of the SPRY1 and tandem-repeat domains at 1.2-1.5 Å resolution, which reveal several structural elements not detected in recent cryo-EM reconstructions of RyRs. The cryo-EM studies disagree on the position of SPRY domains, which had been proposed based on homology modelling. Computational docking of the crystal structures, combined with FRET studies, show that the SPRY1 domain is located next to FK506-binding protein (FKBP). Molecular dynamics flexible fitting and mutagenesis experiments suggest a hydrophobic cluster within SPRY1 that is crucial for FKBP binding. A RyR1 disease mutation, N760D, appears to directly impact FKBP binding through interfering with SPRY1 folding.

  16. Population data of 17 short tandem repeat loci in 2923 individuals from the Han population of Nantong in East China.

    PubMed

    Yang, Min; Li, Liming; Han, Haijun; Jin, Li; Jia, Dongtao; Li, Shilin

    2016-09-01

    Nantong is located in mid-eastern China, and the Han population in Nantong may be greatly affected by population admixture between northern and southern Han Chinese populations. In this study, we analyzed 17 autosomal short tandem repeat (STR) loci on 2923 unrelated individuals collected from the Han population of Nantong. No significant deviation from Hardy-Weinberg equilibrium was observed at all STR loci, and the expected heterozygosity ranged from 0.6184 to 0.9187. The combined match probability (CMP) was 3.87 × 10(-21), and the combined power of discrimination (CPD) was 99.999999999999999999613 %. No significant difference of allele frequencies was observed between Nantong and other Han populations at all STR loci, as well as Dai, Mongolian, and Tibetan. Significant differences were only observed between Nantong Han and Uyghur at TH01, as well as Nantong Han and Dong at CSF1PO and FGA. Nantong Han showed significant differences between She, Bouyei, and Miao at multiple STR loci. PMID:26932871

  17. Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola.

    PubMed

    Zhao, Shuai; Poulin, Lucie; Rodriguez-R, Luis M; Serna, Natalia Forero; Liu, Shu-Yan; Wonni, Issa; Szurek, Boris; Verdier, Valérie; Leach, Jan E; He, Yong-Qiang; Feng, Jia-Xun; Koebnik, Ralf

    2012-10-01

    Xanthomonas oryzae pv. oryzicola is an important bacterial pathogen responsible for outbreaks of bacterial leaf streak (BLS) on rice, mostly occurring in Asia and parts of Africa. To better monitor epidemics and assess population structures, efficient tools that allow the precise identification and diagnosis of pathogenic populations are needed. In this study, we explored variable numbers of tandem repeats (VNTR) as a fast, reliable, and cost-effective molecular typing tool. Screening of three X. oryzae pv. oryzicola genome sequences (Philippine strain BLS256, Chinese strain GX01, and Malian strain MAI10) predicted 28 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 28 loci were designed and applied to a panel of 20 X. oryzae pv. oryzicola strains originating from Asia and Africa. Sequencing of PCR amplicons revealed 25 robust and polymorphic VNTR loci that are shared among Asian and African X. oryzae pv. oryzicola strains. A dendrogram constructed from 25 VNTR loci indicated that most Asian strains are clearly discriminated from African strains. However, in agreement with previous reports, one strain from Mali is related to Asian strains, pointing to a possible introduction of Asian strains to the African continent. The new VNTR-based tool described here is useful for studies of population structures and epidemiological monitoring of X. oryzae pv. oryzicola. PMID:22957820

  18. The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

    PubMed

    Zou, Zheng-Ting; Uphyrkina, Olga V; Fomenko, Pavel; Luo, Shu-Jin

    2015-07-01

    Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied "tigrisPlex" to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples. PMID:25950598

  19. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.

    PubMed

    Quilez, Javier; Guilmatre, Audrey; Garg, Paras; Highnam, Gareth; Gymrek, Melissa; Erlich, Yaniv; Joshi, Ricky S; Mittelman, David; Sharp, Andrew J

    2016-05-01

    Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome. PMID:27060133

  20. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

    PubMed Central

    Dugas, Diana V.; Hernandez, David; Koenen, Erik J.M.; Schwarz, Erika; Straub, Shannon; Hughes, Colin E.; Jansen, Robert K.; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T.; Hajrah, Nahid H.; Alharbi, Njud S.; Al-Malki, Abdulrahman L.; Sabir, Jamal S. M.; Bailey, C. Donovan

    2015-01-01

    The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms. PMID:26592928

  1. Crystal structures of Ryanodine Receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant

    PubMed Central

    Yuchi, Zhiguang; Wong King Yuen, Siobhan M.; Lau, Kelvin; Underhill, Ainsley Q.; Cornea, Razvan L.; Fessenden, James D.; Van Petegem, Filip

    2015-01-01

    Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca2+-dependent signaling events, and consist of several globular domains that together form a large assembly. Here we describe the crystal structures of the SPRY1 and tandem-repeat domains at 1.2 – 1.5Å resolution, which reveal several structural elements not detected in recent cryo-EM reconstructions of RyRs. The cryo-EM studies disagree on the position of SPRY domains, which had been proposed based on homology modeling. Computational docking of the crystal structures, combined with FRET studies, show that the SPRY1 domain is located next to FK506-Binding Protein (FKBP). Molecular dynamics flexible fitting and mutagenesis experiments suggest a hydrophobic cluster within SPRY1 that is crucial for FKBP binding. A RyR1 disease mutation, N760D, appears to directly impact FKBP binding through interfering with SPRY1 folding. PMID:26245150

  2. Cross Protection against Influenza A Virus by Yeast-Expressed Heterologous Tandem Repeat M2 Extracellular Proteins.

    PubMed

    Lee, Yu-Na; Kim, Min-Chul; Lee, Young-Tae; Hwang, Hye Suk; Lee, Jongsang; Kim, Cheol; Kang, Sang-Moo

    2015-01-01

    The influenza M2 ectodomain (M2e) is well conserved across human influenza A subtypes, but there are few residue changes among avian and swine origin influenza A viruses. We expressed a tandem repeat construct of heterologous M2e sequences (M2e5x) derived from human, swine, and avian origin influenza A viruses using the yeast expression system. Intramuscular immunization of mice with AS04-adjuvanted M2e5x protein vaccines was effective in inducing M2e-specific antibodies reactive to M2e peptide and native M2 proteins on the infected cells with human, swine, or avian influenza virus, mucosal and systemic memory cellular immune responses, and cross-protection against H3N2 virus. Importantly, M2e5x immune sera were found to confer protection against different subtypes of H1N1 and H5N1 influenza A viruses in naïve mice. Also, M2e5x-immune complexes of virus-infected cells stimulated macrophages to secrete cytokines via Fc receptors, indicating a possible mechanism of protection. The present study provides evidence that M2e5x proteins produced in yeast cells could be developed as a potential universal influenza vaccine. PMID:26366729

  3. Cross Protection against Influenza A Virus by Yeast-Expressed Heterologous Tandem Repeat M2 Extracellular Proteins

    PubMed Central

    Lee, Yu-Na; Kim, Min-Chul; Lee, Young-Tae; Hwang, Hye Suk; Lee, Jongsang; Kim, Cheol; Kang, Sang-Moo

    2015-01-01

    The influenza M2 ectodomain (M2e) is well conserved across human influenza A subtypes, but there are few residue changes among avian and swine origin influenza A viruses. We expressed a tandem repeat construct of heterologous M2e sequences (M2e5x) derived from human, swine, and avian origin influenza A viruses using the yeast expression system. Intramuscular immunization of mice with AS04-adjuvanted M2e5x protein vaccines was effective in inducing M2e-specific antibodies reactive to M2e peptide and native M2 proteins on the infected cells with human, swine, or avian influenza virus, mucosal and systemic memory cellular immune responses, and cross-protection against H3N2 virus. Importantly, M2e5x immune sera were found to confer protection against different subtypes of H1N1 and H5N1 influenza A viruses in naïve mice. Also, M2e5x-immune complexes of virus-infected cells stimulated macrophages to secrete cytokines via Fc receptors, indicating a possible mechanism of protection. The present study provides evidence that M2e5x proteins produced in yeast cells could be developed as a potential universal influenza vaccine. PMID:26366729

  4. Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system.

    PubMed

    van der Gaag, Kristiaan J; de Leeuw, Rick H; Hoogenboom, Jerry; Patel, Jaynish; Storts, Douglas R; Laros, Jeroen F J; de Knijff, Peter

    2016-09-01

    Current forensic DNA analysis predominantly involves identification of human donors by analysis of short tandem repeats (STRs) using Capillary Electrophoresis (CE). Recent developments in Massively Parallel Sequencing (MPS) technologies offer new possibilities in analysis of STRs since they might overcome some of the limitations of CE analysis. In this study 17 STRs and Amelogenin were sequenced in high coverage using a prototype version of the Promega PowerSeq™ system for 297 population samples from the Netherlands, Nepal, Bhutan and Central African Pygmies. In addition, 45 two-person mixtures with different minor contributions down to 1% were analysed to investigate the performance of this system for mixed samples. Regarding fragment length, complete concordance between the MPS and CE-based data was found, marking the reliability of MPS PowerSeq™ system. As expected, MPS presented a broader allele range and higher power of discrimination and exclusion rate. The high coverage sequencing data were used to determine stutter characteristics for all loci and stutter ratios were compared to CE data. The separation of alleles with the same length but exhibiting different stutter ratios lowers the overall variation in stutter ratio and helps in differentiation of stutters from genuine alleles in mixed samples. All alleles of the minor contributors were detected in the sequence reads even for the 1% contributions, but analysis of mixtures below 5% without prior information of the mixture ratio is complicated by PCR and sequencing artefacts. PMID:27347657

  5. Genetic polymorphism of the 26 short tandem repeat loci in the Chinese Hebei Han population using two commercial forensic kits.

    PubMed

    Lei, Liang; Xu, Jie; Du, Qingqing; Fu, Lihong; Zhang, Xiaojing; Yu, Feng; Ma, Chunling; Cong, Bin; Li, Shujin

    2015-01-01

    We determined the allele frequencies and forensic parameters for the 26 short tandem repeat (STR) autosomal markers in two commercial kits (the Investigator HDplex and AmpFLSTR(®) Identifiler(®) systems) for 183 unrelated individuals from the Han population of the Hebei Province of China. The 26 STRs were all in Hardy-Weinberg equilibrium. No linkage disequilibrium was detected between any pair of loci. The combined power of discrimination and the combined power of exclusion for the 26 STR loci were 1-7.74E-31 and 1-1.21E-11, respectively. Six rare alleles of D10S2325 were identified and named 20, 21, 22, 23, 24, and 31. All the length of the six rare alleles were out of the range of allelic ladder. We calculated the population pairwise genetic distance based on the allele frequencies, using published population data including German, central Polish, south Dutch, northeastern Polish, south Brazilian, Korean, Sichuan Han of China, and Shanghai Han of China. Also we examined the population pairwise genetic distance of loci included in Identifiler system between Hebei Han and other ethnic population of China. These 26 autosomal STR loci could provide highly informative polymorphic data for paternity testing and forensic identification in the Hebei Han population in China. Because they are all in linkage equilibrium, they could be used together to solve deficient kinship cases or cases with mutations. PMID:25262358

  6. Molecular typing of Argentinian Mycobacterium avium subsp. paratuberculosis isolates by multiple-locus variable number-tandem repeat analysis

    PubMed Central

    Gioffré, Andrea; Correa Muñoz, Magnolia; Alvarado Pinedo, María F.; Vaca, Roberto; Morsella, Claudia; Fiorentino, María Andrea; Paolicchi, Fernando; Ruybal, Paula; Zumárraga, Martín; Travería, Gabriel E.; Romano, María Isabel

    2015-01-01

    Multiple-locus variable number-tandem repeat analysis (MLVA) of Mycobacterium avium subspecies paratuberculosis (MAP) isolates may contribute to the knowledge of strain diversity in Argentina. Although the diversity of MAP has been previously investigated in Argentina using IS900-RFLP, a small number of isolates were employed, and a low discriminative power was reached. The aim of the present study was to test the genetic diversity among MAP isolates using an MLVA approach based on 8 repetitive loci. We studied 97 isolates from cattle, goat and sheep and could describe 7 different patterns: INMV1, INMV2, INMV11, INMV13, INMV16, INMV33 and one incomplete pattern. INMV1 and INMV2 were the most frequent patterns, grouping 76.3% of the isolates. We were also able to demonstrate the coexistence of genotypes in herds and co-infection at the organism level. This study shows that all the patterns described are common to those described in Europe, suggesting an epidemiological link between the continents. PMID:26273274

  7. Association between Interleukin-1 Receptor Antagonist (IL1RN) Variable Number of Tandem Repeats (VNTR) Polymorphism and Pulmonary Tuberculosis.

    PubMed

    Hashemi, Mohammad; Naderi, Mohammad; Ebrahimi, Mahboubeh; Amininia, Shadi; Bahari, Gholamreza; Taheri, Mohsen; Eskandari-Nasab, Ebrahim; Ghavami, Saeid

    2015-02-01

    Macrophages and T-lymphocytes are involved in immune response to Mycobacterium tuberculosis. Macrophage produces interleukin (IL)-1 as an inflammatory mediator. IL-1 receptor antagonist (IL1-Ra) is a natural antagonist of IL-1 receptors. In this study we aimed to examine the possible association between the variable number of tandem repeats (VNTR) of the IL-1 receptor antagonist (IL1RN) gene and pulmonary tuberculosis (TB) in a sample of Iranian population. Our study is a case-control study and we examined the VNTR of the IL1RN gene in 265 PTB and 250 healthy subjects by PCR. Neither the overall chi-square comparison of PTB and control subjects nor the logistic regression analysis indicated any association between VNTR IL1RN polymorphism and PTB. Our data suggest that VNTR IL1RN polymorphism may not be associated with the risk of PTB in a sample of Iranian population. Larger studies with different ethnicities are needed to find out the impact of IL1RN VNTR polymorphism on risk of developing TB. PMID:25530139

  8. Evolutionary History of the PER3 Variable Number of Tandem Repeats (VNTR): Idiosyncratic Aspect of Primate Molecular Circadian Clock

    PubMed Central

    Sabino, Flávia Cal; Ribeiro, Amanda Oliveira; Tufik, Sérgio; Torres, Laila Brito; Oliveira, José Américo; Mello, Luiz Eugênio Araújo Moraes; Cavalcante, Jeferson Souza; Pedrazzoli, Mario

    2014-01-01

    The PER3 gene is one of the clock genes, which function in the core mammalian molecular circadian system. A variable number of tandem repeats (VNTR) locus in the 18th exon of this gene has been strongly associated to circadian rhythm phenotypes and sleep organization in humans, but it has not been identified in other mammals except primates. To better understand the evolution and the placement of the PER3 VNTR in a phylogenetical context, the present study enlarges the investigation about the presence and the structure of this variable region in a large sample of primate species and other mammals. The analysis of the results has revealed that the PER3 VNTR occurs exclusively in simiiforme primates and that the number of copies of the primitive unit ranges from 2 to 11 across different primate species. Two transposable elements surrounding the 18th exon of PER3 were found in primates with published genome sequences, including the tarsiiforme Tarsius syrichta, which lacks the VNTR. These results suggest that this VNTR may have evolved in a common ancestor of the simiiforme branch and that the evolutionary copy number differentiation of this VNTR may be associated with primate simiiformes sleep and circadian phenotype patterns. PMID:25222750

  9. First Worldwide Proficiency Study on Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Complex Strains

    PubMed Central

    de Beer, Jessica L.; Kremer, Kristin; Ködmön, Csaba; Supply, Philip

    2012-01-01

    Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency study on 24-locus VNTR typing. Sets of 30 DNAs of MTBC strains, including 10 duplicate DNA samples, were distributed among 37 participating laboratories in 30 different countries worldwide. Twenty-four laboratories used an in-house-adapted method with fragment sizing by gel electrophoresis or an automated DNA analyzer, nine laboratories used a commercially available kit, and four laboratories used other methods. The intra- and interlaboratory reproducibilities of VNTR typing varied from 0% to 100%, with averages of 72% and 60%, respectively. Twenty of the 37 laboratories failed to amplify particular VNTR loci; if these missing results were ignored, the number of laboratories with 100% interlaboratory reproducibility increased from 1 to 5. The average interlaboratory reproducibility of VNTR typing using a commercial kit was better (88%) than that of in-house-adapted methods using a DNA analyzer (70%) or gel electrophoresis (50%). Eleven laboratories using in-house-adapted manual typing or automated typing scored inter- and intralaboratory reproducibilities of 80% or higher, which suggests that these approaches can be used in a reliable way. In conclusion, this first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future. PMID:22170917

  10. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans

    PubMed Central

    Quilez, Javier; Guilmatre, Audrey; Garg, Paras; Highnam, Gareth; Gymrek, Melissa; Erlich, Yaniv; Joshi, Ricky S.; Mittelman, David; Sharp, Andrew J.

    2016-01-01

    Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome. PMID:27060133

  11. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.

    PubMed

    Dugas, Diana V; Hernandez, David; Koenen, Erik J M; Schwarz, Erika; Straub, Shannon; Hughes, Colin E; Jansen, Robert K; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T; Hajrah, Nahid H; Alharbi, Njud S; Al-Malki, Abdulrahman L; Sabir, Jamal S M; Bailey, C Donovan

    2015-01-01

    The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms. PMID:26592928

  12. Multi-locus variable number tandem repeat analysis of Vibrio cholerae isolates from 2012 to 2013 cholera outbreaks in Iran.

    PubMed

    Ranjbar, R; Sadeghy, J; Shokri Moghadam, M; Bakhshi, B

    2016-08-01

    Cholera remains to be an international threat, with high rates of illness and death. In 2012 and 2013, two cholera outbreak happened in Iran, affecting lots of people. Vibrio cholerae O1 was confirmed as the etiological agent. Source identification and controlling the spread of the cholera disease are two critical approaches in cholera outbreaks. In this study, thirty V. cholerae O1 isolates were selected and has been evaluated for antimicrobial resistant as well as molecular typing by multilocus variable-number tandem-repeat analysis (MLVA) method. Twenty-nine (97%) isolates were sero-grouped as El Tor (one isolate was classical) and 100% were related to Inaba serotype. All of the isolates were susceptible to ciprofloxacin, chloramphenicol, ampicillin and gentamicin. On the other hand, 60% of the isolates were MDR (resistant to 3 or more classes). There were three resistance patterns. The most prevalent pattern was resistance to streptomycin, erythromycin, trimethoprim-sulfamethoxazole, and tetracycline (ST-SXT-E-T) which was seen in 50% of isolates. Using MLVA method 14 MLVA types were identified. MLVA type 2 (5-7-7-16-15) accounted for 43% of isolates. Isolates with the same genotype often did not have the same antibiogram. Overall, the data indicate that the Iranian V. cholerae were MDR and clonaly related. Furthermore, the results of this study shows that MLVA can be used as useful method for V. cholerae genotyping in epidemiological investigations. PMID:27247094

  13. Use of an Automated Multiple-Locus, Variable-Number Tandem Repeat-Based Method for Rapid and High-Throughput Genotyping of Staphylococcus aureus Isolates

    PubMed Central

    Francois, Patrice; Huyghe, Antoine; Charbonnier, Yvan; Bento, Manuela; Herzig, Sébastien; Topolski, Ivan; Fleury, Bénédicte; Lew, Daniel; Vaudaux, Pierre; Harbarth, Stephan; van Leeuwen, Willem; van Belkum, Alex; Blanc, Dominique S.; Pittet, Didier; Schrenzel, Jacques

    2005-01-01

    Fast and reliable genotyping methods that allow real-time epidemiological surveillance would be instrumental to monitoring of the spread of methicillin-resistant Staphylococcus aureus. We describe an automated variable-number tandem repeat-based method for the rapid genotyping of Staphylococcus aureus. Multiplex PCR amplifications with eight primer pairs that target gene regions with variable numbers of tandem repeats were resolved by microcapillary electrophoresis and automatically assessed by cluster analysis. This genotyping technique was evaluated for its discriminatory power and reproducibility with clinical isolates of various origins, including a panel of control strains previously characterized by several typing methods and collections from either long-term carriers or defined nosocomial outbreaks. All steps of this new procedure were developed to ensure a rapid turnaround time and moderate cost. The results obtained suggest that this rapid approach is a valuable tool for the genotyping of S. aureus isolates in real time. PMID:16000459

  14. cDNA cloning and mRNA expression of a tandem-repeat galectin (PoGal2) from the pearl oyster, Pinctada fucata.

    PubMed

    Zhang, D C; Hu, Y T; Guo, H Y; Cui, S G; Su, T F; Jiang, S G

    2011-01-01

    Galectins can recognize and specifically bind to β-galactoside residues, playing crucial roles in innate immune responses of vertebrates and invertebrates. We cloned the cDNA of a tandem-repeat galectin from the pearl oyster Pinctada fucata (designated as PoGal2). PoGal2 cDNA is 1347 bp long and consists of a 5'-untranslated region (UTR) of 3 bp, a 3'-UTR of 297 bp with one cytokine RNA instability motif (ATTTA), and an open reading frame of 1047 bp, encoding a polypeptide of 349 amino acids, with an estimated molecular mass of 38.1 kDa and a theoretical isoelectric point of 8.5. PoGal2 contains two carbohydrate recognition domains (CRDs); both have the conserved carbohydrate-binding motifs H-NPR and WG-EE. PoGal2 shares 50.6 and 50.9% identity with those of abalone (Haliotis discus) and the Manila clam (Venerupis philippinarum), respectively. Phylogenetic analysis revealed that the tandem-repeat galectins formed two clades for the different species. Molluscan tandem-repeat galectins were clustered into a single clade, and nematode tandem-repeat galectins were clustered into another single clade. In both clades, CRD-N and CRD-C were divided into different groups. PoGal2 mRNA was constitutively expressed in all tissues analyzed, and the expression level of PoGal2 mRNA was found to be significantly up-regulated in digestive glands, gills and hemocytes after Vibrio alginolyticus stimulation/infection. Expression profile analysis showed that the expression level of PoGal2 mRNA was significantly up-regulated at 8, 12 and 24 h after V. alginolyticus infection. These results suggest that PoGal2 is a constitutive and inducible acute-phase protein involved in the innate immune response of pearl oysters. PMID:21948759

  15. Implementation of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Loci in Mycobacterium tuberculosis Molecular Epidemiology.

    PubMed

    Trovato, Alberto; Tafaj, Silva; Battaglia, Simone; Alagna, Riccardo; Bardhi, Donika; Kapisyzi, Perlat; Bala, Silvana; Haldeda, Migena; Borroni, Emanuele; Hafizi, Hasan; Cirillo, Daniela Maria

    2016-02-01

    This study shows that the addition of a consensus 4-locus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) loci to the spoligotyping-24-locus MIRU-VNTR typing strategy is a well-standardized approach that can contribute to an improvement of the true cluster definition while retaining high typeability in non-Beijing strains. PMID:26659207

  16. Intergenic Variable-Number Tandem-Repeat Polymorphism Upstream of rocA Alters Toxin Production and Enhances Virulence in Streptococcus pyogenes.

    PubMed

    Zhu, Luchang; Olsen, Randall J; Horstmann, Nicola; Shelburne, Samuel A; Fan, Jia; Hu, Ye; Musser, James M

    2016-07-01

    Variable-number tandem-repeat (VNTR) polymorphisms are ubiquitous in bacteria. However, only a small fraction of them has been functionally studied. Here, we report an intergenic VNTR polymorphism that confers an altered level of toxin production and increased virulence in Streptococcus pyogenes The nature of the polymorphism is a one-unit deletion in a three-tandem-repeat locus upstream of the rocA gene encoding a sensor kinase. S. pyogenes strains with this type of polymorphism cause human infection and produce significantly larger amounts of the secreted cytotoxins S. pyogenes NADase (SPN) and streptolysin O (SLO). Using isogenic mutant strains, we demonstrate that deleting one or more units of the tandem repeats abolished RocA production, reduced CovR phosphorylation, derepressed multiple CovR-regulated virulence factors (such as SPN and SLO), and increased virulence in a mouse model of necrotizing fasciitis. The phenotypic effect of the VNTR polymorphism was nearly the same as that of inactivating the rocA gene. In summary, we identified and characterized an intergenic VNTR polymorphism in S. pyogenes that affects toxin production and virulence. These new findings enhance understanding of rocA biology and the function of VNTR polymorphisms in S. pyogenes. PMID:27141081

  17. Analysis of Short Tandem Repeat and Single Nucleotide Polymorphism Loci From Single-Source Samples Using a Custom HaloPlex Target Enrichment System Panel.

    PubMed

    Wendt, Frank R; Zeng, Xiangpei; Churchill, Jennifer D; King, Jonathan L; Budowle, Bruce

    2016-06-01

    Short tandem repeats and single nucleotide polymorphisms (SNPs) are used to individualize biological evidence samples. Short tandem repeat alleles are characterized by size separation during capillary electrophoresis (CE). Massively parallel sequencing (MPS) offers an alternative that can overcome limitations of the CE. With MPS, libraries are prepared for each sample, entailing target enrichment and bar coding, purification, and normalization. The HaloPlex Target Enrichment System (Agilent Technologies) uses a capture-based enrichment system with restriction enzyme digestion to generate fragments containing custom-selected markers. It offers another possible workflow for typing reference samples. Its efficacy was assessed using a panel of 275 human identity SNPs, 88 short tandem repeats, and amelogenin. The data analyzed included locus typing success, depth of sequence coverage, heterozygote balance, and concordance. The results indicate that the HaloPlex Target Enrichment System provides genetic data similar to that obtained by conventional polymerase chain reaction-CE methods with the advantage of analyzing substantially more markers in 1 sequencing run. The genetic typing performance of HaloPlex is comparable to other MPS-based sample preparation systems that utilize primer-based target enrichment. PMID:27075592

  18. Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis

    PubMed Central

    Techaruvichit, Punnida; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

    2015-01-01

    Campylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation of C. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring of C. jejuni and investigation of epidemics caused by C. jejuni. PMID:26025899

  19. Multilocus variable-number tandem-repeat analysis for genotyping of Shigella sonnei strains isolated from pediatric patients

    PubMed Central

    Ranjbar, Reza; Memariani, Mojtaba

    2015-01-01

    Aim: The aims of this study were to characterize Iranian Shigella sonnei strains isolated from pediatric cases and evaluate the utility of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) for genotyping of local S. sonnei strains. Background: S.  sonnei has become the dominant species in certain parts of Iran. Although PFGE is still a gold standard for genotyping and source tracking of food-borne pathogens, it is laborious, expensive, time-consuming, and often difficult to interpret. However, MLVA is a PCR-based method, which is rapid, relatively inexpensive and easy to perform. Patients and methods: A total of 47 S. sonnei isolates were obtained from sporadic cases of pediatric shigellosis in Tehran, Iran, during the years 2002-2003 (n=10) and 2008-2010 (n=37). The patients suffered from acute diarrhea and had evidence of more than three episodes of watery, loose, or bloody stools per day. A MLVA scheme based on 7 VNTR loci was established to assess the diversity of 47 S. sonnei isolates. Results: Based on the results, it was clear that the S. sonnei isolates were heterogeneous. Overall, 47 S. sonnei isolates were discriminated into 21 different genotypes. Analysis of the MLVA profiles using a minimum spanning tree (MST) algorithm showed the usefulness of the MLVA assay in discriminating S. sonnei isolates collected over different time periods. However, no correlation was found between the MLVA genotypes and age, gender or clinical symptoms of the patients. Conclusion: It is assumed that our S. sonnei isolates are derived from a limited number of clones that undergo minor genetic changes in the course of time. The present study has provided some valuable insights into the genetic relatedness of S. sonnei in Tehran, Iran. PMID:26328045

  20. A tandem-repeat galectin-9 involved in immune response of yellow catfish, Pelteobagrus fulvidraco, against Aeromonas hydrophila.

    PubMed

    Wang, Yun; Ke, Fei; Ma, Jingjing; Zhou, Shuaibang

    2016-04-01

    Galectins exclusively recognize and bind β-galactoside on cell surface by carbohydrate recognition domain (CRD). In spite of extensive study of mammalian galectin importance in immune system, little is known about that of fish. To study the immune response of yellow catfish to pathogens, a tandem-repeat galectin-9 from yellow catfish was identified and named PfGAL9. Its full-length cDNA was 1314 bp, including a 117 bp of 5' untranslated region (UTR), a 951 bp of open reading frame (ORF), and a 246 bp of 3' UTR. The ORF encoded 316 amino acids (35.12 KDa), shared the highest 78% identity with the predicted galectin-9 of Ictalurus punctatus. This protein possessed two distinct CRDs with two highly conserved sugar binding motifs. Quantitative PCR showed that PfGAL9 was lowly expressed in skin, gill, fin, muscle, heart, and intestine, highly expressed in tested immune tissues (head kidney, trunk kidney, liver, spleen, and blood) in normal body. After inactivated Aeromonas hydrophila challenge, PfGAL9 was remarkably increased in head kidney and liver in a time-dependent manner. The recombinant protein was expressed in Escherichia coli, which not only agglutinated but also bond all examined bacteria. The binding activities are consistent with the size of aggregates formed by agglutinated bacteria. The agglutination must depend on its direct interaction with bacteria. These results suggested that PfGAL9 was involved in the innate immune response against bacterial infection and clearance of pathogens in yellow catfish. PMID:26892795

  1. Characterisation of Brucella suis isolates from Southeast Europe by multi-locus variable-number tandem repeat analysis.

    PubMed

    Duvnjak, Sanja; Račić, Ivana; Špičić, Silvio; Zdelar-Tuk, Maja; Reil, Irena; Cvetnić, Željko

    2015-10-22

    Porcine brucellosis is a common bacterial zoonosis which can cause significant financial losses. Its diverse and often complicated factors have hampered efforts to control disease spread. The aim of the study was to assess the epidemiological situation of porcine brucellosis primarily in Croatia and its relationship to genotypes present in other, mostly European countries. One hundred and seven Brucella suis strains isolated from swine, hares, cattle, humans, wild hares, a wild boar and a mare originating mainly from Croatia (112), but also a few from Slovenia, Bosnia and Herzegovina, Serbia and Macedonia (15) were tested using classical microbiological testing, Bruce-ladder, RFLP, Multiplex-suis and genotyped using multi-locus variable-number tandem repeat analysis (MLVA). We determined 43 Brucella suis genotypes. Strains were grouped according to phylogenetic and geographic relationships, revealing both regional specificity and uniqueness and suggesting possible sources and modes of spread among animals. Our study also confirmed problems with Bruce19 locus that may hinder comparisons of new types with those in the international database. Forty-one novel genotypes were identified and deposited into the international database. Our study supports the idea of wild animals as a source of disease in domestic animals and also gives evidence to hypothesis of cross-border animal trafficking between former Yugoslavian countries. It also highlights the need to expand such research across more of southeast Europe, especially to countries with poorer social and economical situation in order to prevent a realistic outbreak and for better understanding of the biology of this pathogen. PMID:26324171

  2. The EmsB Tandemly Repeated Multilocus Microsatellite: a New Tool To Investigate Genetic Diversity of Echinococcus granulosus Sensu Lato▿

    PubMed Central

    Maillard, S.; Gottstein, B.; Haag, K. L.; Ma, S.; Colovic, I.; Benchikh-Elfegoun, M. C.; Knapp, J.; Piarroux, R.

    2009-01-01

    Cystic echinococcosis (CE) is a widespread and severe zoonotic disease caused by infection with the larval stage of the eucestode Echinococcus granulosus sensu lato. The polymorphism exhibited by nuclear and mitochondrial markers conventionally used for the genotyping of different parasite species and strains does not reach the level necessary for the identification of genetic variants linked to restricted geographical areas. EmsB is a tandemly repeated multilocus microsatellite that proved its usefulness for the study of genetic polymorphisms within the species E. multilocularis, the causative agent of alveolar echinococcosis. In the present study, EmsB was used to characterize E. granulosus sensu lato samples collected from different host species (sheep, cattle, dromedaries, dogs, and human patients) originating from six different countries (Algeria, Mauritania, Romania, Serbia, Brazil, and the People's Republic of China). The conventional mitochondrial cox1 and nad1 markers identified genotypes G1, G3, G5, G6, and G7, which are clustered into three groups corresponding to the species E. granulosus sensu stricto, E. ortleppi, and E. canadensis. With the same samples, EmsB provided a higher degree of genetic discrimination and identified variations that correlated with the relatively small-scale geographic origins of the samples. In addition, one of the Brazilian single hydatid cysts presented a hybrid genotypic profile that suggested genetic exchanges between E. granulosus sensu stricto and E. ortleppi. In summary, the EmsB microsatellite exhibits an interesting potential for the elaboration of a detailed map of the distribution of genetic variants and therefore for the determination and tracking of the source of CE. PMID:19741078

  3. The EmsB tandemly repeated multilocus microsatellite: a new tool to investigate genetic diversity of Echinococcus granulosus sensu lato.

    PubMed

    Maillard, S; Gottstein, B; Haag, K L; Ma, S; Colovic, I; Benchikh-Elfegoun, M C; Knapp, J; Piarroux, R

    2009-11-01

    Cystic echinococcosis (CE) is a widespread and severe zoonotic disease caused by infection with the larval stage of the eucestode Echinococcus granulosus sensu lato. The polymorphism exhibited by nuclear and mitochondrial markers conventionally used for the genotyping of different parasite species and strains does not reach the level necessary for the identification of genetic variants linked to restricted geographical areas. EmsB is a tandemly repeated multilocus microsatellite that proved its usefulness for the study of genetic polymorphisms within the species E. multilocularis, the causative agent of alveolar echinococcosis. In the present study, EmsB was used to characterize E. granulosus sensu lato samples collected from different host species (sheep, cattle, dromedaries, dogs, and human patients) originating from six different countries (Algeria, Mauritania, Romania, Serbia, Brazil, and the People's Republic of China). The conventional mitochondrial cox1 and nad1 markers identified genotypes G1, G3, G5, G6, and G7, which are clustered into three groups corresponding to the species E. granulosus sensu stricto, E. ortleppi, and E. canadensis. With the same samples, EmsB provided a higher degree of genetic discrimination and identified variations that correlated with the relatively small-scale geographic origins of the samples. In addition, one of the Brazilian single hydatid cysts presented a hybrid genotypic profile that suggested genetic exchanges between E. granulosus sensu stricto and E. ortleppi. In summary, the EmsB microsatellite exhibits an interesting potential for the elaboration of a detailed map of the distribution of genetic variants and therefore for the determination and tracking of the source of CE. PMID:19741078

  4. Clostridium botulinum group I strain genotyping by 15-locus multilocus variable-number tandem-repeat analysis.

    PubMed

    Fillo, Silvia; Giordani, Francesco; Anniballi, Fabrizio; Gorgé, Olivier; Ramisse, Vincent; Vergnaud, Gilles; Riehm, Julia M; Scholz, Holger C; Splettstoesser, Wolf D; Kieboom, Jasper; Olsen, Jaran-Strand; Fenicia, Lucia; Lista, Florigio

    2011-12-01

    Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of C. botulinum isolates of any BoNT type is relevant for both epidemiological studies and forensic microbiology. A 10-locus multiple-locus variable-number tandem-repeat analysis (MLVA) was previously applied to isolates of C. botulinum type A. The present study includes five additional loci designed to better address proteolytic B and F serotypes. We investigated 79 C. botulinum group I strains isolated from human and food samples in several European countries, including types A (28), B (36), AB (4), and F (11) strains, and 5 nontoxic Clostridium sporogenes. Additional data were deduced from in silico analysis of 10 available fully sequenced genomes. This 15-locus MLVA (MLVA-15) scheme identified 86 distinct genotypes that clustered consistently with the results of amplified fragment length polymorphism (AFLP) and MLVA genotyping in previous reports. An MLVA-7 scheme, a subset of the MLVA-15, performed on a lab-on-a-chip device using a nonfluorescent subset of primers, is also proposed as a first-line assay. The phylogenetic grouping obtained with the MLVA-7 does not differ significantly from that generated by the MLVA-15. To our knowledge, this report is the first to analyze genetic variability among all of the C. botulinum group I serotypes by MLVA. Our data provide new insights into the genetic variability of group I C. botulinum isolates worldwide and demonstrate that this group is genetically highly diverse. PMID:22012011

  5. Clostridium botulinum Group I Strain Genotyping by 15-Locus Multilocus Variable-Number Tandem-Repeat Analysis ▿ †

    PubMed Central

    Fillo, Silvia; Giordani, Francesco; Anniballi, Fabrizio; Gorgé, Olivier; Ramisse, Vincent; Vergnaud, Gilles; Riehm, Julia M.; Scholz, Holger C.; Splettstoesser, Wolf D.; Kieboom, Jasper; Olsen, Jaran-Strand; Fenicia, Lucia; Lista, Florigio

    2011-01-01

    Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of C. botulinum isolates of any BoNT type is relevant for both epidemiological studies and forensic microbiology. A 10-locus multiple-locus variable-number tandem-repeat analysis (MLVA) was previously applied to isolates of C. botulinum type A. The present study includes five additional loci designed to better address proteolytic B and F serotypes. We investigated 79 C. botulinum group I strains isolated from human and food samples in several European countries, including types A (28), B (36), AB (4), and F (11) strains, and 5 nontoxic Clostridium sporogenes. Additional data were deduced from in silico analysis of 10 available fully sequenced genomes. This 15-locus MLVA (MLVA-15) scheme identified 86 distinct genotypes that clustered consistently with the results of amplified fragment length polymorphism (AFLP) and MLVA genotyping in previous reports. An MLVA-7 scheme, a subset of the MLVA-15, performed on a lab-on-a-chip device using a nonfluorescent subset of primers, is also proposed as a first-line assay. The phylogenetic grouping obtained with the MLVA-7 does not differ significantly from that generated by the MLVA-15. To our knowledge, this report is the first to analyze genetic variability among all of the C. botulinum group I serotypes by MLVA. Our data provide new insights into the genetic variability of group I C. botulinum isolates worldwide and demonstrate that this group is genetically highly diverse. PMID:22012011

  6. Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

    PubMed

    Much, Melissa; Buza, Natalia; Hui, Pei

    2014-03-01

    Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences. PMID:24444463

  7. Evaluation of factor VIII polymorphic short tandem repeat markers in linkage analysis for carrier diagnosis of hemophilia A

    PubMed Central

    Shrestha, Sabina; Dong, Sufang; Li, Zuhua; Huang, Zhuliang; Zheng, Fang

    2016-01-01

    Hemophilia A (HA) is the most common inherited X-linked recessive bleeding disorder caused by heterogeneous mutations in the factor VIII gene (FVIII). Diagnosis of the carrier is critical for preventing the birth of children affected by this coagulation disorder, which ultimately facilitates its management. Due to the heterogeneous nature of mutations, the large inversions and the complexity of the FVIII gene, direct recognition of the disease-associated mutation in HA is complex. Indirect linkage analysis using highly informative heterozygous polymorphic markers is an alternative method for determining the co-segregation of the mutant gene within a family for carrier detection of HA. The aim of the present study was to perform carrier diagnosis in a family with HA. Rapid multifluorescent polymerase chain reaction (PCR) was performed with six extragenic short tandem repeats (STRs), DXS1073, DXS15, DXS8091, DXS1227, DXS991, DXS993 and one intragenic marker, STR22 for linkage analysis in the HA family. All the STR markers employed in the present study were informative for linkages of pathogenic and healthy haplotypes among family members, particularly STR22, DXS1073 and DXS15. The STR marker, STR22, is within the FVIII gene while the DXS1073 and DXS15 markers are very close to the FVIII gene, where the chances of recombination are comparatively low, and provided the most accurate interpretation analysis, indicating that the proband's sister may have been the HA carrier. Rapid multifluorescent PCR using STR markers and linkage analysis was identified to be a simple method for performing HA carrier diagnosis. PMID:27446547

  8. Multiple-locus variable-number tandem-repeat analysis of Brucella isolates from patients in Xinjiang China

    PubMed Central

    Zhang, Fengbo; Li, Zhiwei; La, Xiaolin; Ma, Xiumin; Zhang, Yaoxin; Ji, Ping; Jiang, Min; Hu, Jinwei; Zhang, Zhaoxia; Lu, Xiaobo; Ding, Jianbing

    2015-01-01

    Objective: This study is to characterize and identify the human Brucella strains in Xinjiang, China with multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) scheme. Methods: Brucella strains were isolated and cultured from 62 brucellosis patients. The bacteria strains were subjected to the oxidase, catalase, rapid urease, and nitrate reduction tests, and the species identification was performed using the VITEK-2 Compact system. These Brucella strains were further identified and characterized using the 16 VNTR loci in a MLVA-16 methodology. Results: Twelve Brucella strains had been identified out of 62 patients, which were all recognized as Brucella melitensis (B. melitensis) according to the results from the VITEK-2 Compact system. Based on panel 1 (MLVA-8), these 12 Brucella isolates were clustered into three known genotypes and two new genotypes, in which 7 strains were clustered into genotype 45 (1-5-3-12-2-2-3-2), 1 strain was classified as genotype 42 (1-5-3-13-2-2-3-2), 1 stain was with genotype 62 (1-3-3-13-2-2-3-2), and the other 3 trains revealed two new genotypes, i.e., (1-5-3-12-2-3-3-2) and (1-5-3-11-2-3-3-2). Using panel 2A+2B (MLVA-16), we found that no genotypes of these strains were identical to the known genotypes, generally with differences in 2-4 loci. However, three strains shared the same genotype. Conclusion: Brucella strains in 62 brucellosis patients from Xinjiang are all identified as B. melitensis. Based on MLVA-8, two new genotypes have been discovered. These findings might contribute to the understanding of the pathogenesis and epidemiology of brucellosis in Xinjiang, China. PMID:26629067

  9. CYP2C9 Promoter Variable Number Tandem Repeat Polymorphism Regulates mRNA Expression in Human Livers

    PubMed Central

    Sun, Xiaochun; Gong, Yan; Gawronski, Brian E.; Langaee, Taimour Y.; Shahin, Mohamed Hossam A.; Khalifa, Sherief I.; Johnson, Julie A.

    2012-01-01

    CYP2C9 is involved in metabolism of nearly 25% of clinically used drugs. Coding region polymorphisms CYP2C9*2 and *3 contribute to interperson variability in drug dosage and clinical outcomes, whereas the role of a regulatory polymorphism remains uncertain. Measuring allelic RNA expression in 87 human liver samples, combined with genotyping, sequencing, and reporter gene assays, we identified a promoter variable number tandem repeat polymorphism (pVNTR) that fully accounted for allelic CYP2C9 mRNA expression differences. Present in three different variant forms [short (pVNTR-S), medium (pVNTR-M), and long (pVNTR-L)], only the pVNTR-S allele reduced the CYP2C9 mRNA level compared with the pVNTR-M (reference) allele. pVNTR-S is in linkage disequilibrium with *3, with linkage disequilibrium r2 of 0.53 to 0.75 in different populations. In patients who were taking a maintenance dose of warfarin, the mean warfarin dose was associated with the copies of pVNTR-S (p = 0.0001). However, in multivariate regression models that included the CYP2C9*3, pVNTR-S was no longer a significant predictor of the warfarin dose (p = 0.60). These results indicate that although pVNTR-S reduced CYP2C9 mRNA expression, the in vivo effects of pVNTR-S on warfarin metabolism cannot be separated from the effects of *3. Therefore, it is not necessary to consider pVNTR-S as an additional biomarker for warfarin dosing. Larger clinical studies are needed to define whether the pVNTR-S has a minimal effect in vivo, or whether the effect attributed to *3 is really a combination of effects on expression by the pVNTR-S along with effects on catalytic activity from the nonsynonymous *3 variant. PMID:22289258

  10. Mutational analysis of 33 autosomal short tandem repeat (STR) loci in southwest Chinese Han population based on trio parentage testing.

    PubMed

    Jin, Bo; Su, Qin; Luo, Haibo; Li, Yingbi; Wu, Jin; Yan, Jing; Hou, Yiping; Liang, Weibo; Zhang, Lin

    2016-07-01

    Mutation rates and 95% CI of 33 short tandem repeat (STR) loci (D1S2142, D2S1338, D2S441, D3S1358, D3S1754, D5S818, D6S1043, D7S3048, D7S820, D8S1132, D8S1179, D10S1248, D11S2368, D12S391, D13S1492, D13S317, D13S325, D14S306, D15S659, D16S539, D18S1364, D18S51, D19S433, D20S161, D21S11, D22GATA198B05, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA) were investigated through more than 424,000 parent-child meiotic transfers obtained from 10636 trios parentage testing cases in southwest Chinese Han population. Overall, 297, including 292 single-step, 4 double-step and 1 triple-step mutation events were observed. The average mutation rate was 0.70×10(-3). Most of the locus-specific mutation rates (varied from 0.20×10(-3) to 1.96×10(-3)) were lower than the other datasets (p<0.05). Mutations of 7 loci are reported for the first time. Mutation rates varied with population from different ethnicities and geographical regions. There was no significant difference between mutation expansion and contraction (∼1.04:1). Paternal origin mutations occurred more frequently than maternal origin ones (∼5.02:1). In addition, mutation rates indicated positive correlation with the expected heterozygosity (He) and geometric mean of longest run of perfect repeats (LRPR), respectively. Short alleles showed a trend toward mutation gain while long alleles trended toward mutation loss. A credible forensic dataset for locus-specific mutation rates of 33 loci has been established based upon strict inclusion criteria of large-sized parents/child-trio cases. PMID:27045978

  11. Allelic ladder characterization of the short tandem repeat polymorphism located in the 5{prime} flanking region to the human coagulation factor XIII A subunit gene

    SciTech Connect

    Puers, C.; Lins, A.M.; Sprecher, C.J.

    1994-09-01

    The short tandem repeat (STR) polymorphism present within the 5{prime} untranslated region of the human coagulation factor XIII A subunit gene, HUM-F13A01 [AAAG]{sub n}, was evaluated using an allelic ladder, i.e., a standard size marker consisting of amplified alleles from the locus. The allelic ladder was constructed by pooling 12 polymerase chain reaction (PCR)-amplified alleles identified by their differential migration in denaturing polyacrylamide gel electrophoresis. This standard marker was used to distinguish 14 different alleles observed at this locus. Sequence analyses indicate that 13 of the alleles contain 4 through 16 iterations of the tandemly repeated AAAG sequence, respectively. The remaining allele carries four repeats and displays a deletion of two consecutive nucleotides (GT), one base distal to the repeat region. The allelic ladder was employed to type 326 F13A01 chromosomes rapidly and reliably in representatives of a German Caucasian population. Population data were analyzed with respect to Hardy-Weinberg Equilibrium (HWE) and compared with those of a previously studied Houston, Texas, Caucasian population. 27 refs., 2 figs., 1 tab.

  12. Application of variable-number tandem-repeat typing to discriminate Ralstonia solanacearum strains associated with English watercourses and disease outbreaks.

    PubMed

    Parkinson, Neil; Bryant, Ruth; Bew, Janice; Conyers, Christine; Stones, Robert; Alcock, Michael; Elphinstone, John

    2013-10-01

    Variable-number tandem-repeat (VNTR) analysis was used for high-resolution discrimination among Ralstonia solanacearum phylotype IIB sequevar 1 (PIIB-1) isolates and further evaluated for use in source tracing. Five tandem-repeat-containing loci (comprising six tandem repeats) discriminated 17 different VNTR profiles among 75 isolates from potato, geranium, bittersweet (Solanum dulcamara), tomato, and the environment. R. solanacearum isolates from crops at three unrelated outbreak sites where river water had been used for irrigation had distinct VNTR profiles that were shared with PIIB-1 isolates from infected bittersweet growing upriver of each site. The VNTR profiling results supported the implication that the source of R. solanacearum at each outbreak was contaminated river water. Analysis of 51 isolates from bittersweet growing in river water at different locations provided a means to evaluate the technique for studying the epidemiology of the pathogen in the environment. Ten different VNTR profiles were identified among bittersweet PIIB-1 isolates from the River Thames. Repeated findings of contiguous river stretches that produced isolates that shared single VNTR profiles supported the hypothesis that the pathogen had disseminated from infected bittersweet plants located upriver. VNTR profiles shared between bittersweet isolates from two widely separated Thames tributaries (River Ray and River Colne) suggested they were independently contaminated with the same clonal type. Some bittersweet isolates had VNTR profiles that were shared with potato isolates collected outside the United Kingdom. It was concluded that VNTR profiling could contribute to further understanding of R. solanacearum epidemiology and assist in control of future disease outbreaks. PMID:23892739

  13. Haplotype frequencies of 17 Y-chromosomal short tandem repeat loci from the Cukurova region of Turkey

    PubMed Central

    Serin, Ayse; Canan, Husniye; Alper, Behnan; Sertdemir, Yasar

    2011-01-01

    Aim To investigate the distribution of 17 Y-short tandem repeat (STR) loci in the population of the Cukurova region of Turkey. Methods In the period between 2009 and 2010, we investigated the distribution of 17 Y-STRs in a sample of 249 unrelated healthy men from the Cukurova region of Turkey. Genomic DNA was extracted with InstaGene matrix and Y-STRs were determined using the AmpFISTR Yfiler PCR amplification kit. Gene and haplotype diversity values were estimated using the Arlequin software. To compare our data to other populations, population pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Web site software. Results At 17 Y-STR loci we detected 148 alleles. The lowest gene diversity in this region was 0.51 for DYS391 and the highest 0.95 for DYS385a/b. Haplotype diversity was 0.9997 ± 0.0004. We compared our data with haplotype data of other Turkish populations and no significant differences were found, except with Ankara population (Φst = 0.025, P = 0.018). Comparisons were also made with the neighboring populations using analysis of molecular variance of the Y-STR loci genetic structure and our population was nearest to Lenkoran-Azerbaijani (Φst = 0.012, P = 0.068) and Iranian Ahvaz population (Φst = 0.007, P = 0.173), followed by Greek (Φst = 0.026, P = 0.000) and Russian (Φst = 0.048, P = 0.000) population. Other countries like Portugal, Spain, Italy, Egypt, Israel (Palestinian Authority Area), and Taiwan showed a high genetic distance from our population. Conclusion Our study showed that Y-STR polymorphisms were a powerful discrimination tool for routine forensic applications and could be used in genealogical investigations. PMID:22180269

  14. Authentication of newly established human esophageal squamous cell carcinoma cell line (YM-1) using short tandem repeat (STR) profiling method.

    PubMed

    Ayyoob, Khosravi; Masoud, Khoshnia; Vahideh, Kazeminejad; Jahanbakhsh, Asadi

    2016-03-01

    Cross-contamination during or early after establishment of a new cell line could result in the worldwide spread of a misidentified cell line. Therefore, newly established cell lines need to be authenticated by a reference standard method. This study was conducted to investigate the authenticity of a newly established epithelial cell line of human esophageal squamous cell carcinoma (ESCC) called YM-1 using short tandem repeat (STR) DNA profiling method. Primary human ESCC epithelial cells were cultured from the fresh tumor tissue of an adult female patient. Growth characteristics and epithelial originality of YM-1 cells were studied. Genomic DNA was isolated from YM-1 cells harvested at passage 22 and ESCC donor tumor sample on two different days to prevent probable DNA contamination. STR profiling was performed using AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. To address whether YM-1 cells undergo genetic alteration as the passage number increases, STR profiling was performed again on harvested cells at passage 51. YM-1 cells grew as a monolayer with a population doubling time of 40.66 h. Epithelial originality of YM-1 cells was confirmed using ICC/IF staining of cytokeratins AE1/AE3. The STR profile of the ESCC donor tumor sample was the same with YM-1 cells at passage 22. However, STR profile of the donor tumor sample showed an off-ladder (OL) allele in their D7S820 locus. Also, re-profiling of YM-1 cells at passage 51 showed a loss of heterozygosity (LOH) at D18S51 locus. This suggests that long-term culture of cell lines may alter their DNA profile. Comparison of the DNA fingerprinting results in DSMZ, and ATCC STR profiling databases confirmed unique identity of YM-1 cell line. This study provides an easy, fast, and reliable procedure for authentication of newly established cell lines, which helps in preventing the spread of misidentified cells and improving the reproducibility and validity of experiments, consequently. PMID:26432330

  15. Case-control study of allele frequencies of 15 short tandem repeat loci in males with impulsive violent behavior

    PubMed Central

    Yang, Chun; Ba, Huajie; Gao, Zhiqin; Zhao, Hanqing; Yu, Haiying; Guo, Wei

    2013-01-01

    Background Analysis of genetic polymorphisms in short tandem repeats (STRs) is an accepted method for detecting associations between genotype and phenotype but it has not previously been used in the study of the genetics of impulsive violent behavior. Objective Compare the prevalence of different polymorphisms in 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) between men with a history of impulsive violence and male control subjects without a history of impulsive violence. Methods The distributions of the alleles of the 15 STR loci were compared between 407 cases with impulsive violent behavior and 415 controls using AmpFlSTR® Identifiler™ kits. Results Compared to controls, the average frequencies of the following alleles were significantly lower in individuals with a history of violent behavior: allele 10 of TH01 (OR=0.29, 95%CI=0.16-0.52, p<0.0001,), allele 8 of TPOX (OR=0.71, 95%CI=0.58-0.86, p=0.0005), allele 9 of TPOX (OR=0.65, 95%CI=0.47-0.89, p=0.0072) and allele 14 of CSF1PO (OR=0.27, 95%CI=0.11-0.68, p=0.0035). One allele was significantly higher in cases than controls: allele 11 of TPOX (OR=1.79, 95%CI=1.45-2.22, p<0.0001). Conclusions To the best of our knowledge, this is the first behavioral genetic study that clearly demonstrates a close relationship between specific genetic markers and impulsive aggression in non-psychiatric offenders. Further prospective work will be needed to determine whether or not the alleles identified can be considered risk factors for impulsive aggression and, if so, the underlying mechanisms that result in this relationship. PMID:24991178

  16. Multiple-locus variable-number tandem repeat analysis and clinical characterization of Leptospira interrogans canine isolates.

    PubMed

    Koizumi, Nobuo; Muto, Maki Mizutani; Izumiya, Hidemasa; Suzuki, Motoi; Ohnishi, Makoto

    2015-03-01

    Canine leptospirosis occurs worldwide; however, information on the relationship between Leptospira serotypes/genotypes and virulence in dogs remains limited. We investigated the molecular characteristics of Leptospira interrogans canine isolates belonging to three serogroups using multiple-locus variable-number tandem repeat analysis (MLVA) and the effects of each serotype/genotype on the clinical characteristics of leptospirosis in dogs. MLVA using 11 loci of the three major L. interrogans serogroups in Japan, Australis (32 strains from 21 dogs), Autumnalis (12; 7) and Hebdomadis (66; 39), revealed more divergent genetic heterogeneity within each serogroup than multilocus sequence typing (MLST), and they formed two, three and five clusters (CLs), respectively. Lethal infections were caused by all Leptospira serogroup isolates (70.3 % with Hebdomadis, 83.3 % with Australis and 100 % with Autumnalis) or Leptospira isolates belonging to all the CLs (57.1-100 %) without any significant differences. A significant difference in hyperaemia and haemorrhage of mucus membrane was observed between serogroups Australis and Autumnalis (P = 0.03). Leptospira isolates of Australis CL2 caused no hyperaemia and haemorrhage from mucus membrane, whereas those of Australis CL1, Autumnalis CL3 and Hebdomadis CL1 and CL3 did (P<0.05). Significant differences in creatinine (Cre) levels were observed between serogroups Australis and Hebdomadis (P = 0.02). In addition, significant differences in blood urea nitrogen levels were observed between serogroups Australis and Hebdomadis (P = 0.004) and Australis and Autumnalis (P = 0.02). Based on MLVA types, a significant difference in Cre levels was observed between Hebdomadis CL1 and CL4 (P = 0.0018). Our results indicated that MLVA had a higher discriminatory power and was more concordant with serotyping than MLST. Although all Leptospira serotypes and genotypes caused lethal infections in dogs, the L. interrogans

  17. Multilocus variable-number tandem-repeat genotyping of Renibacterium salmoninarum, a bacterium causing bacterial kidney disease in salmonid fish

    PubMed Central

    2013-01-01

    Background Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, is a bacterial disease of fish, which is both geographically widespread and difficult to control. Previously, application of various molecular typing methods has failed to reliably discriminate between R. salmoninarum isolates originating from different host species and geographic areas. The current study aimed to utilize multilocus variable number tandem repeats (VNTR) to investigate inter-strain variation of R. salmoninarum to establish whether host-specific populations exist in Atlantic salmon and rainbow trout respectively. Such information would be valuable in risk assessment of transmission of R. salmoninarum in a multispecies aquaculture environment. Results The present analysis utilizing sixteen VNTRs distinguished 17 different haplotypes amongst 41 R. salmoninarum isolates originating from Atlantic salmon and rainbow trout in Scotland, Norway and the US. The VNTR typing system revealed two well supported groups of R. salmoninarum haplotypes. The first group included R. salmoninarum isolates originating from both Atlantic salmon and rainbow trout circulating in Scottish and Norwegian aquaculture, in addition to the type strain ATCC33209T originating from Chinook salmon in North America. The second group comprised isolates found exclusively in Atlantic salmon, of mainly wild origin, including isolates NCIB1114 and NCIB1116 associated with the original Dee disease in Scotland. Conclusions The present study confirmed that VNTR analysis can be successfully applied to discriminate R. salmoninarum strains. There was no clear distinction between isolates originating from Atlantic salmon and rainbow trout as several haplotypes in group 1 clustered together R. salmoninarum isolates from both species. These findings indicate a potential exchange of pathogens between Atlantic salmon and rainbow trout in Scottish and Norwegian aquaculture during the last 20 years. In a scenario of

  18. Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile

    PubMed Central

    Lin, Jer-Young; Jacobus, Barbara Hass; SanMiguel, Phillip; Walling, Jason G.; Yuan, Yinan; Shoemaker, Randy C.; Young, Nevin D.; Jackson, Scott A.

    2005-01-01

    Little is known about the physical makeup of heterochromatin in the soybean (Glycine max L. Merr.) genome. Using DNA sequencing and molecular cytogenetics, an initial analysis of the repetitive fraction of the soybean genome is presented. BAC 076J21, derived from linkage group L, has sequences conserved in the pericentromeric heterochromatin of all 20 chromosomes. FISH analysis of this BAC and three subclones on pachytene chromosomes revealed relatively strict partitioning of the heterochromatic and euchromatic regions. Sequence analysis showed that this BAC consists primarily of repetitive sequences such as a 102-bp tandem repeat with sequence identity to a previously characterized ∼120-bp repeat (STR120). Fragments of Calypso-like retroelements, a recently inserted SIRE1 element, and a SIRE1 solo LTR were present within this BAC. Some of these sequences are methylated and are not conserved outside of G. max and G. soja, a close relative of soybean, except for STR102, which hybridized to a restriction fragment from G. latifolia. These data present a picture of the repetitive fraction of the soybean genome that is highly concentrated in the pericentromeric regions, consisting of rapidly evolving tandem repeats with interspersed retroelements.

  19. Human G-protein-coupled inwardly rectifying potassium channel (GIRK1) gene (KCNJ3): Localization to chromosome 2 and identification of a simple tandem repeat polymorphism

    SciTech Connect

    Stoffel, M.; Powell, K.L.; Espinosa, R. III; Philipson, L.H.; Le Beau, M.M.; Bell, G.I. )

    1994-05-01

    The gene encoding the human G-protein-coupled inwardly rectifying potassium channel designated GIRK1 (gene symbol, KCNJ3) was mapped to chromosome 2 by analyzing its segregation in a panel of human-hamster somatic cell hybrids. This assignment was confirmed by fluorescence in situ hybridization to metaphase chromosomes, and the gene was further localized to band 2q24.1. A highly informative simple tandem repeat DNA polymorphism of the form (CA)[sub n] was identified and used to localize KCNJ3 within the genetic map of the long arm of chromosome 2. 8 refs., 1 fig., 2 tabs.

  20. Identification of a novel tandemly repeated sequence present in an intron of the glucose phosphate isomerase (GPI) gene in mouse and man

    SciTech Connect

    Faik, P.; Walker, J.I.H.; Morgan, M.J. )

    1994-05-01

    Glucose phosphate isomerase (GPI, glucose 6-phosphate ketol-isomerase, EC 5.3.1.9) is a housekeeping gene expressed in all tissues and organisms that utilize glycolysis and gluconeogenesis. Deficiency in humans leads to a rare form of nonspherocytic hemolytic anemia. The authors have isolated a 3.2-kb mouse cDNA containing glucose phosphate isomerase coding sequence and a 2.1-kb intronic sequence and a large proportion of the human gene (approaching 55 kb) in four phage [lambda] recombinants. A 4-kb intronic fragment from the human gene showing homology to the mouse intronic sequence has been isolated and sequenced. The fragment contains approximately 1.5 kb of sequence that is composited of 30 repeat units of a novel 50-kb tandemly repeated unit. The mouse intronic sequence contains 18 similar units. The human consensus sequence differs from the mouse consensus sequence at only 7 positions out of 50 (positions 16, 26, 27, 42, 43, 47, and 48). A probe containing the repeat element detects polymorphisms, specific to glucose phosphate isomerase, in human DNA. The repeat element does not appear to be present at any other loci in human DNA. The conservation of this intronic repeat element extends to pig and Chinese hamster. 26 refs., 4 figs.

  1. The human gene (CSNK2A1) coding for the casein kinase II subunit [alpha] is located on chromosome 20 and contains tandemly arranged Alu repeats

    SciTech Connect

    Wirkner, U.; Lichter, P.; Pyerin, W. ); Voss, H.; Ansorge, W. )

    1994-01-15

    The authors have isolated and characterized an 18.9-kb genomic clone representing a central portion of the human casein kinase II (CKII) subunit [alpha] gene (CSNK2A1). Using the whole clone as a probe, the gene was localized on chromosome 20p13. The clone contains eight exons whose sequences comprise bases 102 to 824 of the coding region of the human CKII[alpha]. The exon/intron splice junctions conform to the gt/ag rule. Three of the nine introns are located at positions corresponding to those in the CKII[alpha] gene of the nematode Caenorhabditis elegans. The introns contain eight complete and eight incomplete Alu repeats. Some of the Alu sequences are arranged in tandems of two or three, which seem to originate from insertions of younger Alu sequences into the poly(A) region of previously integrated Alu sequences, as indicated by flanking direct repeats. 50 refs., 5 figs., 1 tab.

  2. Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont “Candidatus Liberibacter asiaticus” as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats ▿ †

    PubMed Central

    Zhou, Lijuan; Powell, Charles A.; Hoffman, Michele T.; Li, Wenbin; Fan, Guocheng; Liu, Bo; Lin, Hong; Duan, Yongping

    2011-01-01

    “Candidatus Liberibacter asiaticus” is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of “Ca. Liberibacter” associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (hyvI and hyvII) were identified in the prophage regions of the Psy62 “Ca. Liberibacter asiaticus” genome. Sequence analyses of the hyvI and hyvII genes in 35 “Ca. Liberibacter asiaticus” DNA isolates collected globally revealed that the hyvI gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while hyvII contains up to 2 NITRs and 4 partial repeats and shares homology with hyvI. Frequent deletions or insertions of these repeats within the hyvI and hyvII genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of “Ca. Liberibacter asiaticus” bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single “Ca. Liberibacter asiaticus”-infected sample. This is the first evidence of different “Ca. Liberibacter asiaticus” populations coexisting in a single HLB-affected sample. The Florida “Ca. Liberibacter asiaticus” isolates contain both hyvI and hyvII, while all other global “Ca. Liberibacter asiaticus” isolates contain either one or the other. Interclade assignments of the putative HyvI and HyvII proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple “Ca. Liberibacter asiaticus” populations in the world and a multisource introduction of the “Ca. Liberibacter asiaticus” bacterium into Florida. PMID:21784907

  3. A variable number of tandem repeats in the 3'-untranslated region of the dopamine transporter modulates striatal function during working memory updating across the adult age span.

    PubMed

    Sambataro, Fabio; Podell, Jamie E; Murty, Vishnu P; Das, Saumitra; Kolachana, Bhaskar; Goldberg, Terry E; Weinberger, Daniel R; Mattay, Venkata S

    2015-08-01

    Dopamine modulation of striatal function is critical for executive functions such as working memory (WM) updating. The dopamine transporter (DAT) regulates striatal dopamine signaling via synaptic reuptake. A variable number of tandem repeats in the 3'-untranslated region of SLC6A3 (DAT1-3'-UTR-VNTR) is associated with DAT expression, such that 9-repeat allele carriers tend to express lower levels (associated with higher extracellular dopamine concentrations) than 10-repeat homozygotes. Aging is also associated with decline of the dopamine system. The goal of the present study was to investigate the effects of aging and DAT1-3'-UTR-VNTR on the neural activity and functional connectivity of the striatum during WM updating. Our results showed both an age-related decrease in striatal activity and an effect of DAT1-3'-UTR-VNTR. Ten-repeat homozygotes showed reduced striatal activity and increased striatal-hippocampal connectivity during WM updating relative to the 9-repeat carriers. There was no age by DAT1-3'-UTR-VNTR interaction. These results suggest that, whereas striatal function during WM updating is modulated by both age and genetically determined DAT levels, the rate of the age-related decline in striatal function is similar across both DAT1-3'-UTR-VNTR genotype groups. They further suggest that, because of the baseline difference in striatal function based on DAT1-3'-UTR-VNTR polymorphism, 10-repeat homozygotes, who have lower levels of striatal function throughout the adult life span, may reach a threshold of decreased striatal function and manifest impairments in cognitive processes mediated by the striatum earlier in life than the 9-repeat carriers. Our data suggest that age and DAT1-3'-UTR-VNTR polymorphism independently modulate striatal function. PMID:25997640

  4. Isolation, characterization, and bioinformatic analysis of calmodulin-binding protein cmbB reveals a novel tandem IP22 repeat common to many Dictyostelium and Mimivirus proteins.

    PubMed

    O'Day, Danton H; Suhre, Karsten; Myre, Michael A; Chatterjee-Chakraborty, Munmun; Chavez, Sara E

    2006-08-01

    A novel calmodulin-binding protein cmbB from Dictyostelium discoideum is encoded in a single gene. Northern analysis reveals two cmbB transcripts first detectable at 4 h during multicellular development. Western blotting detects an approximately 46.6 kDa protein. Sequence analysis and calmodulin-agarose binding studies identified a "classic" calcium-dependent calmodulin-binding domain (179IPKSLRSLFLGKGYNQPLEF198) but structural analyses suggest binding may not involve classic alpha-helical calmodulin-binding. The cmbB protein is comprised of tandem repeats of a newly identified IP22 motif ([I,L]Pxxhxxhxhxxxhxxxhxxxx; where h = any hydrophobic amino acid) that is highly conserved and a more precise representation of the FNIP repeat. At least eight Acanthamoeba polyphaga Mimivirus proteins and over 100 Dictyostelium proteins contain tandem arrays of the IP22 motif and its variants. cmbB also shares structural homology to YopM, from the plague bacterium Yersenia pestis. PMID:16777069

  5. Complete mitochondrial genome of Coelomactra antiquata (Mollusca: Bivalvia): The first representative from the family Mactridae with novel gene order and unusual tandem repeats.

    PubMed

    Meng, Xueping; Zhao, Nana; Shen, Xin; Hao, Jue; Liang, Meng; Zhu, Xiaolin; Cheng, Hanliang; Yan, Binlun; Liu, Zhaopu

    2012-06-01

    The complete mitochondrial genome plays an important role in the accurate inference of phylogenetic relationships among metazoans. Mactridae, also known as trough shells or duck clams, is an important family of marine bivalve clams in the order Veneroida. Here we present the complete mitochondrial genome sequence of the Xishishe Coelomactra antiquata (Mollusca: Bivalvia), which is the first representative from the family Mactridae. The mitochondrial genome of C. antiquata is of 17,384bp in length, and encodes 35 genes, including 12 protein-coding, 21 transfer RNA, and 2 ribosomal RNA genes. Compared with the typical gene content of animal mitochondrial genomes, atp8 and tRNAS(2) are missing. Gene order of the mitochondrial genome of C. antiquata is unique compared with others from Veneroida. In the mitochondrial genome of the C. antiquata, a total of 2189bp of non-coding nucleotides are scattered among 26 non-coding regions. The largest non-coding region contains one section of tandem repeats (99 bp×11), which is the second largest tandem repeats found in the mitochondrial genomes from Veneroida. The phylogenetic trees based on mitochondrial genomes support the monophyly of Veneridae and Lucinidae, and the relationship at the family level: ((Veneridae+Mactridae)+(Cardiidae+Solecurtidae))+Lucinidae. The phylogenetic result is consistent with the morphological classification. Meanwhile, bootstrap values are very high (BP=94-100), suggesting that the evolutionary relationship based on mitochondrial genomes is very reliable. PMID:22381378

  6. Characterisation of human outbreaks of brucellosis and sporadic cases by the use of hyper-variable octameric oligonucleotide fingerprint (HOOF) variable number tandem repeats.

    PubMed

    Valdezate, S; Cervera, I; Hernandez, P; Navarro, A; Saéz Nieto, J A

    2007-09-01

    Hyper-variable octameric oligonucleotide fingerprints (HOOFs) enable typing of Brucella spp. by targeting the 8-bp tandem repeat in eight loci that vary in number (variable number tandem repeats; VNTRs). Brucella is one of the most important zoonotic pathogens, because of its public health and economic consequences. To assess the role of HOOFs as epidemiological markers for Brucella melitensis, which is the main species involved in human brucellosis in Spain, 87 sporadic and outbreak isolates were investigated; these originated from broad or more restricted geographical locations, including unrelated (n = 42), semi-related (n = 19) and closely related (n = 26) groups of isolates. Distinct HOOFs were detected in the entire (n = 74), unrelated (n = 42), semi-related (n = 19) and closely related (n = 13) groups. Seven of the eight VNTR markers investigated identified multiple alleles in the four groups of isolates. Using the composite data for eight VNTRs, a diversity value of 0.98 was calculated for the entire population, taking into account single- and double-locus variants. A high correlation (R = 0.98) between the maximum copy number and the number of alleles was observed. The most polymorphic markers were VNTR-1, VNTR-4, VNTR-5 and VNTR-7 (D > OR = 0.8). Characterisation of B. melitensis isolates by HOOFs enabled the recognition of related human cases and the exchange of molecular epidemiological information concerning a spreading clone, thus improving brucellosis surveillance. PMID:17686139

  7. Multiple-locus variable number of tandem repeats analysis of Salmonella enterica serotype paratyphi A from Yuxi and comparison with isolates from the Chinese Medical Culture Collection Center

    PubMed Central

    YAO, YINGBO; CUI, XIAOYAN; CHEN, QINGSHAN; HUANG, XINRONG; ELMORE, BRADLEY; PAN, QING; WANG, SHUKUN; LIU, JIE

    2014-01-01

    The aim of the present study was to genotype Salmonella enterica serotype paratyphi A (SPA) isolated from Yuxi, China, in a multiple-locus variable number of tandem repeats (VNTRs) analysis (MLVA) and to compare them with isolates from the Chinese Medical Culture Collection Center (CMCC). Potential VNTRs were screened from the genomes of ATCC9150 and AKU_12601 using the Tandem Repeats Finder program. Nine VNTRs were established for MLVA typing of 195 SPA isolates from Yuxi and 20 isolates from CMCC. The dendogram for MLVA profiles and minimum spanning tree (MST) were drawn using the categorical coefficient calculated by BioNumerics software. A total of 23 MLVA types were identified in 215 SPA isolates and were grouped into six distinct cluster groups A, B, C, D, E and F. A total of 195 Yuxi SPA isolates were exclusively grouped into cluster C with nine MLVA genotypes. A total of 20 CMCC isolates were grouped in clusters A B, D, E and F with the other 14 MLVA types. The MLVA with nine VNTR loci, which was exploited in the present study, represents a successful strategy for genotyping SPA. Furthermore, the 195 Yuxi isolates appear to be closely related to each other and distinct from the 20 CMCC strains. PMID:24788795

  8. Multiple-locus variable-number tandem repeat analysis (MLVA) of Leptospira interrogans serovar Pomona from Argentina reveals four new genotypes.

    PubMed

    Pavan, María Elisa; Cairó, Fabián; Brihuega, Bibiana; Samartino, Luis

    2008-01-01

    Outbreaks of leptospirosis occur regularly in Argentina, but little is known about their epidemiological relationships. We have analyzed the genetic diversity of a collection of 16 strains of Leptospira interrogans serovar Pomona isolated from animals and humans in Argentina during the past 45 years. Genotyping was performed by multiple-locus variable-number tandem repeat analysis (MLVA) using the loci VNTR4, VNTR7, VNTR9, VNTR10, VNTR19, VNTR23 and VNTR31, as described by Majed et al. [Identification of variable-number tandem-repeat loci in Leptospira interrogans sensu stricto. J Clin Microbiol 2005;43:539-45]. Clustering analysis revealed four new distinct MLVA genotypes, with a dominant one. Strains with this genotype were consistently isolated since 1960 to the present, mainly from cows and pigs, but also from humans, representing 75% of the total strains studied. These strains coexisted temporally and geographically with isolates presenting the other new genotypes. VNTR4 locus, with four different alleles, presented the highest diversity between the VNTR loci analyzed. MLVA patterns obtained will be useful for future diagnostic and epidemiological tracing analysis. PMID:17531318

  9. Variable-number tandem repeats genotyping used to aid and inform management strategies for a bovine Johne's disease incursion in tropical and subtropical Australia.

    PubMed

    Oakey, Jane; Gavey, Lawrence; Singh, Shoor Vir; Platell, Joanne; Waltisbuhl, David

    2014-09-01

    The application of variable-number tandem repeats (VNTR) genotyping of Mycobacterium avium subsp. paratuberculosis isolates to assist in investigating incidents of bovine Johne's disease in a low-prevalence region of Australia is described in the current study. Isolates from a response to detection of bovine Johne's disease in Queensland were compared with strains from national and international sources. The tandem application of mycobacterial interspersed repetitive unit (MIRU) and multilocus short sequence repeats (MLSSR) genotyping identified 2 strains, 1 that infected cattle on multiple properties with trace-forward histories from a common infected property, and 1 genotypically different strain recovered from a single property. The former strain showed an identical genotype to an isolate from India. Neither strain showed a genotypic link to regions of Australia with a higher prevalence of the disease. Genotyping has indicated incursions from 2 independent sources. This intelligence has informed investigations into potential routes of entry and the soundness of ongoing control measures, and supported strategy and policy decisions regarding management of Mycobacterium avium subsp. paratuberculosis incursions for Queensland. PMID:25139793

  10. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿†

    PubMed Central

    Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo

    2011-01-01

    Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956

  11. Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese

    PubMed Central

    Ebstein, Richard P.; Monakhov, Mikhail V.; Lu, Yunfeng; Jiang, Yushi; Lai, Poh San; Chew, Soo Hong

    2015-01-01

    Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal–conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified. PMID:26246555

  12. Genetic stability of Brucella abortus S19 and RB51 vaccine strains by multiple locus variable number tandem repeat analysis (MLVA16).

    PubMed

    Dorneles, Elaine Maria Seles; de Faria, Ana Paula Paiva; Pauletti, Rebeca Barbosa; Santana, Jordana Almeida; Caldeira, George Afonso Vítor; Heinemann, Marcos Bryan; Titze-de-Almeida, Ricardo; Lage, Andrey Pereira

    2013-10-01

    The aims of the present study were (i) to assess the in vitro genetic stability of S19 and RB51 Brucella abortus vaccines strains and (ii) to evaluate the ability of multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) as a tool to be used in the quality control of live vaccines against brucellosis. Sixty-three batches of commercial S19 (n=53) and RB51 (n=10) vaccines, produced between 2006 and 2009, were used in this study. S19 and RB51 vaccines were obtained from, respectively, seven and two different manufacturers. Ten in vitro serial passages were performed on reference strains and on selected batches of commercial vaccines. All batches, reference strains and strains of serial passages were typed by the MLVA16. The results demonstrated that B. abortus S19 and RB51 vaccine strains are genetically stable and very homogeneous in their respective groups. Anyway, batches of S19 from one manufacturer and batches of RB51 from another presented genotypes distincts from the reference vaccine strains. In both cases, differences were found on locus Bruce07, which had addition of one repeat unit in the case of S19 batches and the deletion of one repeat unit in the case of RB51 batches. In summary, MLVA16 proved to be a molecular tool capable of discriminating small genomic variations and should be included in in vitro official tests. PMID:23933375

  13. A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse.

    PubMed

    Darrow, Emily M; Chadwick, Brian P

    2014-06-01

    The human genome contains numerous large tandem repeats, many of which remain poorly characterized. Here we report a novel transfer RNA (tRNA) tandem repeat on human chromosome 1q23.3 that shows extensive copy number variation with 9-43 repeat units per allele and displays evidence of meiotic and mitotic instability. Each repeat unit consists of a 7.3 kb GC-rich sequence that binds the insulator protein CTCF and bears the chromatin hallmarks of a bivalent domain in human embryonic stem cells. A tRNA containing tandem repeat composed of at least three 7.6-kb GC-rich repeat units reside within a syntenic region of mouse chromosome 1. However, DNA sequence analysis reveals that, with the exception of the tRNA genes that account for less than 6% of a repeat unit, the remaining 7.2 kb is not conserved with the notable exception of a 24 base pair sequence corresponding to the CTCF binding site, suggesting an important role for this protein at the locus. PMID:24753417

  14. A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse

    PubMed Central

    Darrow, Emily M.; Chadwick, Brian P.

    2014-01-01

    The human genome contains numerous large tandem repeats, many of which remain poorly characterized. Here we report a novel transfer RNA (tRNA) tandem repeat on human chromosome 1q23.3 that shows extensive copy number variation with 9–43 repeat units per allele and displays evidence of meiotic and mitotic instability. Each repeat unit consists of a 7.3 kb GC-rich sequence that binds the insulator protein CTCF and bears the chromatin hallmarks of a bivalent domain in human embryonic stem cells. A tRNA containing tandem repeat composed of at least three 7.6-kb GC-rich repeat units reside within a syntenic region of mouse chromosome 1. However, DNA sequence analysis reveals that, with the exception of the tRNA genes that account for less than 6% of a repeat unit, the remaining 7.2 kb is not conserved with the notable exception of a 24 base pair sequence corresponding to the CTCF binding site, suggesting an important role for this protein at the locus. PMID:24753417

  15. A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of the Ralstonia solanacearum species complex

    PubMed Central

    Ravelomanantsoa, Santatra; Robène, Isabelle; Chiroleu, Frédéric; Guérin, Fabien; Poussier, Stéphane; Pruvost, Olivier

    2016-01-01

    Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC

  16. A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of the Ralstonia solanacearum species complex.

    PubMed

    Ravelomanantsoa, Santatra; Robène, Isabelle; Chiroleu, Frédéric; Guérin, Fabien; Poussier, Stéphane; Pruvost, Olivier; Prior, Philippe

    2016-01-01

    Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC

  17. A new variant of endemic pemphigus foliaceus in El-Bagre, Colombia: the Hardy-Weinberg-Castle law and linked short tandem repeats

    PubMed Central

    Abreu-Velez, Ana María; Robles, Edinson Villa; Howard, Michael S.

    2009-01-01

    Background: We reported a new variant of endemic pemphigus foliaceus in El Bagre, Colombia. Aims: Our study performed Complex Segregation Analysis (CSA) and short tandem repeats to discriminate between environmental and/or genetic factors in this disorder. Materials and Methods: The CSA analysis was carried out according to the unified model, implemented using the transmission probabilities implemented in the computer program POINTER, and evaluated by using a software package for population genetic data analysis (GDA), Arlequin. We performed pedigree analyses by using Cyrillic 2.1 software, with a total of 30 families with 50 probands (47 males and 3 females) tested. In parallel to the CSA, we tested for the presence of short tandem repeats from HLA class II, DQ alpha 1, involving the gene locus D6S291 by using the Hardy-Weinberg- Castle law. Results Our results indicate that the best model of inheritance in this disease is a mixed model, with multifactorial effects within a recessive genotype. Two types of possible segregation patterns were found; one with strong recessive penetrance in families whose phenotype is more Amerindian-like, and another of possible somatic mutations. Conclusion: The penetrance of 10% or less in female patients 60 years of age or older indicates that hormones could protect younger females. The greatest risk factor for men being affected by the disorder was the NN genotype. These findings are only possible due to somatic mutations, and/or strong environmental effects. We also found a protective role for two genetic loci (D6S1019 AND D6S439) in the control group. PMID:22666691

  18. Diversity of Y-short tandem repeats in the representative sample of the population of Canton Sarajevo residents, Bosnia and Herzegovina.

    PubMed

    Cenanović, Merisa; Pojskić, Naris; Kovacević, Lejla; Dzehverović, Mirela; Cakar, Jasmina; Musemić, Dzenisa; Marjanović, Damir

    2010-06-01

    In our previous population study, we have used twelve Y-chromosomal short tandem repeats loci incorporated in the PowerPlex Y System to determine Y-STR diversity in B&H human population. With intent to obtain additional verification of the previously obtained results as well as to establish specific reference for a local B&H population, we have decided to test DNA samples collected from 100 unrelated healthy male Canton Sarajevo residents (from Sarajevo region) for the same twelve Y-linked short tandem repeats loci. Qiagen DNeasy Tissue Kit (Qiagen, GmbH, Hilden, Germany) was used for DNA extraction from buccal swabs and PowerPlex Y System (Promega Corp., Madison, WI) has been used to simultaneously amplify Y-STR loci by PCR. PowerPlex Y System includes 12 STR loci: DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. The total PCR reaction volume was 5 microL. PCR amplifications were carried out in PE GeneAmp PCR System Thermal Cycler (ABI). Electrophoresis of the amplification products was preformed on an ABI PRISM 310 genetic analyzer (ABI, Foster City, CA) according to the manufacturer's recommendations. The raw data were compiled and analyzed using the accessory software: ABI PRISM Data Collection Software and Genemapper version 3.2. In addition, we have compared the obtained "Sarajevo" dataset with the data previously generated for the entire Bosnian and Herzegovinian population, as well as with the available data on geographically close (neighboring) European populations. The results of this study will be used as guidelines in additional improving of research into genetic relationship among recent local B&H populations, both isolated and open, which is a long-term project in our country. PMID:20698129

  19. Microfluidic-chip-based multiple-locus variable-number tandem-repeat fingerprinting with new primer sets for methicillin-resistant Staphylococcus aureus.

    PubMed

    Sabat, Artur J; Chlebowicz, Monika A; Grundmann, Hajo; Arends, Jan P; Kampinga, Greetje; Meessen, Nico E L; Friedrich, Alexander W; van Dijl, Jan Maarten

    2012-07-01

    The detection of outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) infections and a rapid and accurate identification of sources and routes of transmission should be conducted in hospital settings as early and swiftly as possible. In this study, we investigated the application potential of a new approach based on multiple-locus variable-number tandem-repeat fingerprinting (MLVF) and microfluidics technology for a rapid discrimination of MRSA lineages in outbreak settings. A total of 206 nonrepetitive MRSA isolates recovered from infected patients at the University Medical Center Groningen between 2000 and 2010 were tested. The results obtained by MLVF using microcapillary electrophoresis with newly designed primers were compared to those obtained by spa typing and multiple-locus variable-number tandem-repeat analysis (MLVA). The discriminatory power was 0.980 (107 patterns), 0.969 (85 allelic profiles), and 0.959 (66 types) for MLVF, MLVA, and spa typing, respectively. All methods tested showed a good concordance of results calculated by the adjusted Rand's coefficient method. Comparisons of data obtained by the three approaches allowed us to propose an 88% cutoff value for the similarity between any two MLVF patterns, which can be used in S. aureus epidemiological studies, including analyses of outbreaks and strain transmission events. Of the three tested methods, MLVF is the cheapest, fastest, and easiest to perform. MLVF applied to microfluidic polymer chips is a rapid, cheap, reproducible, and highly discriminating tool to determine the clonality of MRSA isolates and to trace the spread of MRSA strains over periods of many years. Although spa typing should be used due to its portability of data, MLVF has a high added value because it is more discriminatory. PMID:22573591

  20. Multiple-locus variable-number tandem repeat analysis for strain discrimination of non-O157 Shiga toxin-producing Escherichia coli.

    PubMed

    Timmons, Chris; Trees, Eija; Ribot, Efrain M; Gerner-Smidt, Peter; LaFon, Patti; Im, Sung; Ma, Li Maria

    2016-06-01

    Non-O157 Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens of growing concern worldwide that have been associated with several recent multistate and multinational outbreaks of foodborne illness. Rapid and sensitive molecular-based bacterial strain discrimination methods are critical for timely outbreak identification and contaminated food source traceback. One such method, multiple-locus variable-number tandem repeat analysis (MLVA), is being used with increasing frequency in foodborne illness outbreak investigations to augment the current gold standard bacterial subtyping technique, pulsed-field gel electrophoresis (PFGE). The objective of this study was to develop a MLVA assay for intra- and inter-serogroup discrimination of six major non-O157 STEC serogroups-O26, O111, O103, O121, O45, and O145-and perform a preliminary internal validation of the method on a limited number of clinical isolates. The resultant MLVA scheme consists of ten variable number tandem repeat (VNTR) loci amplified in three multiplex PCR reactions. Sixty-five unique MLVA types were obtained among 84 clinical non-O157 STEC strains comprised of geographically diverse sporadic and outbreak related isolates. Compared to PFGE, the developed MLVA scheme allowed similar discrimination among serogroups O26, O111, O103, and O121 but not among O145 and O45. To more fully compare the discriminatory power of this preliminary MLVA method to PFGE and to determine its epidemiological congruence, a thorough internal and external validation needs to be performed on a carefully selected large panel of strains, including multiple isolates from single outbreaks. PMID:27071532

  1. Evolving diversity of ‘Candidatus Liberibacter asiaticus’ revealed by comparative analysis of two related intragenic tandem repeat genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Candidatus Liberibacter asiaticus’ (Las) is the most prevalent species of the citrus Huanglongbing bacteria. Two related and hyper variable genes (hyvI and hyvII) were identified in the prophage regions of the psy62 Las genome. The hyvI (2760 bp) contains 12 nearly identical 132-bp repeats and 4 pa...

  2. Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae)

    PubMed Central

    Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

    2013-01-01

    Background and Aims The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. Methods A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100–500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Key Results Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S–5·8S–25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. Conclusions The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species. PMID:23666888

  3. Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome

    SciTech Connect

    Lopez, J.V.; Cevario, S.; O`Brien, S.J.

    1996-04-15

    The complete 17,009-bp mitochondrial genome of the domestic cat, Felis catus, has been sequenced and conforms largely to the typical organization of previously characterized mammalian mtDNAs. Codon usage and base composition also followed canonical vertebrate patterns, except for an unusual ATC (non-AUG) codon initiating the NADH dehydrogenase subunit 2 (ND2) gene. Two distinct repetitive motifs at opposite ends of the control region contribute to the relatively large size (1559 bp) of this carnivore mtDNA. Alignment of the feline mtDNA genome to a homologous 7946-bp nuclear mtDNA tandem repeat DNA sequence in the cat, Numt, indicates simple repeat motifs associated with insertion/deletion mutations. Overall DNA sequence divergence between Numt and cytoplasmic mtDNA sequence was only 5.1%. Substitutions predominate at the third codon position of homologous feline protein genes. Phylogenetic analysis of mitochondrial gene sequences confirms the recent transfer of the cytoplasmic mtDNA sequences to the domestic cat nucleus and recapitulates evolutionary relationships between mammal species. 86 refs., 4 figs., 3 tabs.

  4. A Mutator Transposon Insertion Is Associated With Ectopic Expression of a Tandemly Repeated Multicopy Myb Gene pericarp color1 of Maize

    PubMed Central

    Robbins, Michael L.; Sekhon, Rajandeep S.; Meeley, Robert; Chopra, Surinder

    2008-01-01

    The molecular basis of tissue-specific pigmentation of maize carrying a tandemly repeated multicopy allele of pericarp color1 (p1) was examined using Mutator (Mu) transposon-mediated mutagenesis. The P1-wr allele conditions a white or colorless pericarp and a red cob glumes phenotype. However, a Mu-insertion allele, designated as P1-wr-mum6, displayed an altered phenotype that was first noted as occasional red stripes on pericarp tissue. This gain-of-pericarp-pigmentation phenotype was heritable, yielding families that displayed variable penetrance and expressivity. In one fully penetrant family, deep red pericarp pigmentation was observed. Several reports on Mu suppressible alleles have shown that Mu transposons can affect gene expression by mechanisms that depend on transposase activity. Conversely, the P1-wr-mum6 phenotype is not affected by transposase activity. The increased pigmentation was associated with elevated mRNA expression of P1-wr-mum6 copy (or copies) that was uninterrupted by the transposons. Genomic bisulfite sequencing analysis showed that the elevated expression was associated with hypomethylation of a floral-specific enhancer that is ∼4.7 kb upstream of the Mu1 insertion site and may be proximal to an adjacent repeated copy. We propose that the Mu1 insertion interferes with the DNA methylation and related chromatin packaging of P1-wr, thereby inducing expression from gene copy (or copies) that is otherwise suppressed. PMID:18430921

  5. Transcription of two classes of rat growth hormone gene-associated repetitive DNA: differences in activity and effects of tandem repeat structure.

    PubMed Central

    Gutierrez-Hartmann, A; Lieberburg, I; Gardner, D; Baxter, J D; Cathala, G G

    1984-01-01

    The rat growth hormone (rGH) gene contains two classes of repetitive DNA arranged as clusters within intron B and the 3' flanking region. The major family is equivalent to the CHO type 2 DNA. The second ("truncated repeat", TR) is a truncated version of the first and occurs in certain neural-specific transcripts and genes ("identifier" elements, ID). Here we report, using the HeLa cell-free transcription assay, that RNA polymerase III (Pol III) efficiently initiates at internal promoters within a tandem array of rGH gene repetitive DNA monomers and results in a novel organization of overlapping Class III transcription units. Transcription competition studies revealed that the rat type 2 structures share Pol III transcription factors with a tRNA gene, a human Alu repeat, and a mutant VA1 gene. Also, the rGH type 2 but not the TR DNA efficiently promotes Pol III initiation, yet other TR members, which differ only in flanking DNA, are transcribed. Thus, the rGH gene is strikingly enriched with 10 repetitive DNA monomers; multimeric type 2 elements are actively transcribed; rGH-TR sequences are expressed only as part of larger transcripts promoted by type 2 DNA; and, type 2 DNA uses tRNA gene transcription factors. These studies show that flanking sequences, promoter organization and factor competition may all affect rat repetitive DNA expression. Images PMID:6091058

  6. Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat (MIRU-VNTR) Genotyping of Mycobacterium intracellulare for Strain Comparison with Establishment of a PCR-Based Database

    PubMed Central

    Iakhiaeva, Elena; McNulty, Steven; Brown Elliott, Barbara A.; Falkinham, Joseph O.; Williams, Myra D.; Vasireddy, Ravikiran; Wilson, Rebecca W.; Turenne, Christine

    2013-01-01

    Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the “gold standard” of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible. PMID:23175249

  7. Prevalence and molecular characterization of Escherichia coli O157:H7 by multiple locus variable number tandem repeat analysis and pulsed field gel electrophoresis in three sheep farming operations in California.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A yearlong study was conducted to determine the fecal prevalence of Escherichia coli O157:H7 in three sheep ranches. Strain diversity and persistence was compared using multiple locus variable number tandem repeat analysis and pulsed field gel electrophoresis. Ranch C, a feedlot, consisted of young ...

  8. Development of new multilocus variable number of tandem repeat analysis (MLVA) for Listeria innocua and its application in a food processing plant.

    PubMed

    Takahashi, Hajime; Ohshima, Chihiro; Nakagawa, Miku; Thanatsang, Krittaporn; Phraephaisarn, Chirapiphat; Chaturongkasumrit, Yuphakhun; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

    2014-01-01

    Listeria innocua is an important hygiene indicator bacterium in food industries because it behaves similar to Listeria monocytogenes, which is pathogenic to humans. PFGE is often used to characterize bacterial strains and to track contamination source. However, because PFGE is an expensive, complicated, time-consuming protocol, and poses difficulty in data sharing, development of a new typing method is necessary. MLVA is a technique that identifies bacterial strains on the basis of the number of tandem repeats present in the genome varies depending on the strains. MLVA has gained attention due to its high reproducibility and ease of data sharing. In this study, we developed a MLVA protocol to assess L. innocua and evaluated it by tracking the contamination source of L. innocua in an actual food manufacturing factory by typing the bacterial strains isolated from the factory. Three VNTR regions of the L. innocua genome were chosen for use in the MLVA. The number of repeat units in each VNTR region was calculated based on the results of PCR product analysis using capillary electrophoresis (CE). The calculated number of repetitions was compared with the results of the gene sequence analysis to demonstrate the accuracy of the CE repeat number analysis. The developed technique was evaluated using 60 L. innocua strains isolated from a food factory. These 60 strains were classified into 11 patterns using MLVA. Many of the strains were classified into ST-6, revealing that this MLVA strain type can contaminate each manufacturing process in the factory. The MLVA protocol developed in this study for L. innocua allowed rapid and easy analysis through the use of CE. This technique was found to be very useful in hygiene control in factories because it allowed us to track contamination sources and provided information regarding whether the bacteria were present in the factories. PMID:25198191

  9. Ten tandem repeats of {beta}-hCG 109-118 enhance immunogenicity and anti-tumor effects of {beta}-hCG C-terminal peptide carried by mycobacterial heat-shock protein HSP65

    SciTech Connect

    Zhang Yankai; Yan Rong; He Yi; Liu Wentao; Cao Rongyue; Yan Ming; Li Taiming; Liu Jingjing; Wu Jie . E-mail: wu_jie97@yahoo.com.cn

    2006-07-14

    The {beta}-subunit of human chorionic gonadotropin ({beta}-hCG) is secreted by many kinds of tumors and it has been used as an ideal target antigen to develop vaccines against tumors. In view of the low immunogenicity of this self-peptide,we designed a method based on isocaudamer technique to repeat tandemly the 10-residue sequence X of {beta}-hCG (109-118), then 10 tandemly repeated copies of the 10-residue sequence combined with {beta}-hCG C-terminal 37 peptides were fused to mycobacterial heat-shock protein 65 to construct a fusion protein HSP65-X10-{beta}hCGCTP37 as an immunogen. In this study, we examined the effect of the tandem repeats of this 10-residue sequence in eliciting an immune by comparing the immunogenicity and anti-tumor effects of the two immunogens, HSP65-X10-{beta}hCGCTP37 and HSP65-{beta}hCGCTP37 (without the 10 tandem repeats). Immunization of mice with the fusion protein HSP65-X10-{beta}hCGCTP37 elicited much higher levels of specific anti-{beta}-hCG antibodies and more effectively inhibited the growth of Lewis lung carcinoma (LLC) in vivo than with HSP65-{beta}hCGCTP37, which should suggest that HSP65-X10-{beta}hCGCTP37 may be an effective protein vaccine for the treatment of {beta}-hCG-dependent tumors and multiple tandem repeats of a certain epitope are an efficient method to overcome the low immunogenicity of self-peptide antigens.

  10. Tandem repeats, high copy number and remarkable diel expression rhythm of form II RuBisCO in Prorocentrum donghaiense (Dinophyceae).

    PubMed

    Shi, Xinguo; Zhang, Huan; Lin, Senjie

    2013-01-01

    Gene structure and expression regulation of form II RuBisCO (rbcII) in dinoflagellates are still poorly understood. Here we isolated this gene (Pdrbc) and investigated its diel expression pattern in a harmful algal bloom forming dinoflagellate Prorocentrum donghaiense. We obtained cDNA sequences with triple tandem repeats of the coding unit (CU); the 5' region has the sequence of a typical dinoflagellate plastid gene, encoding an N-terminus with two transmembrane regions separated by a plastid transit peptide. The CUs (1,455 bp except 1464 bp in last CU) are connected through a 63 bp spacer. Phylogenetic analysis showed that rbcII CUs within species formed monophyletic clusters, indicative of intraspecific gene duplication or purifying evolution. Using quantitative PCR (qPCR) we estimated 117±40 CUs of Pdrbc in the P. donghaiense genome. Although it is commonly believed that most dinoflagellate genes lack transcriptional regulation, our RT-qPCR analysis on synchronized cultures revealed remarkable diel rhythm of Pdrbc expression, showing significant correlations of transcript abundance with the timing of the dark-to-light transition and cell cycle G2M-phase. When the cultures were shifted to continuous light, Pdrbc expression remained significantly correlated with the G2M-phase. Under continuous darkness the cell cycle was arrested at the G1 phase, and the rhythm of Pdrbc transcription disappeared. Our results suggest that dinoflagellate rbcII 1) undergoes duplication or sequence purification within species, 2) is organized in tandem arrays in most species probably to facilitate efficient translation and import of the encoded enzyme, and 3) is regulated transcriptionally in a cell cycle-dependent fashion at least in some dinoflagellates. PMID:23976999

  11. Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy.

    PubMed Central

    Mariappan, S V; Garcoa, A E; Gupta, G

    1996-01-01

    Anomalous expansion of the DNA triplet (CTG)n causes myotonic dystrophy. Structural studies have been carried out on (CTG)n repeats in an attempt to better understand the molecular mechanism of repeat expansion. NMR and gel electrophoretic studies demonstrate the presence of hairpin structures for (CTG)5 and (CTG)6 in solution. The monomeric hairpin structure remains invariant over a wide range of salt concentrations (10-200 mM NaCl), DNA concentrations (micromolar to millimolar in DNA strand) and pH (6.0-7.5). The (CTG)n hairpin contains three bases in the loop when n is odd and four bases when n is even. For both odd and even n the stacking and pairing in the stem remain the same, i.e, two hydrogen bond T.T pairs stack with the neighboring G.C pairs. All the nucleotides in (CTG)5 and (CTG)6 adopt C2'-endo, anti conformations. Full-relaxation matrix analysis has been performed to derive the NOE distance constraints from NOESY experiments at seven different mixing times (25, 50, 75, 100, 125, 200 and 500 ms). NOESY-derived distance constraints were subsequently used in restrained molecular dynamics simulations to obtain a family of structures consistent with the NMR data. The theoretical order parameters are computed for H5-H6(cytosines) and H2'-H2" dipolar correlations for both (CTG)5 and (CTG)6 by employing the Lipari-Szabo formalism. Experimental data show that the cytosine in the loop of the (CTG)5 hairpin is slightly more flexible than those in the stem. The cytosine in the loop of the (CTG)6 hairpin is extremely flexible, implying that the dynamics of the four base loop is intrinsically different from that of the three base loop. PMID:8604323

  12. High-resolution NMR characterization of a spider-silk mimetic composed of 15 tandem repeats and a CRGD motif

    PubMed Central

    McLachlan, Glendon D; Slocik, Joseph; Mantz, Robert; Kaplan, David; Cahill, Sean; Girvin, Mark; Greenbaum, Steve

    2009-01-01

    Multidimensional solution NMR spectroscopic techniques have been used to obtain atomic level information about a recombinant spider silk construct in hexafluoro-isopropanol (HFIP). The synthetic 49 kDa silk-like protein mimics authentic silk from Nephila clavipes, with the inclusion of an extracellular matrix recognition motif. 2D 1H-15N HSQC NMR spectroscopy reveals 33 cross peaks, which were assigned to amino acid residues in the semicrystalline repeat units. Signals from the amorphous segments in the primary sequence were weak and broad, suggesting that this region is highly dynamic and undergoing conformational exchange. An analysis of the deviations of the 13Cα, 13Cβ, and 13CO chemical shifts relative to the expected random coil values reveals two highly α-helical regions from amino acid 12–19 and 26–32, which comprise the polyalanine track and a GGLGSQ sequence. This finding is further supported by φ-value analysis and sequential and medium-range NOE interactions. Pulsed field gradient NMR measurements indicate that the topology of the silk mimetic in HFIP is nonglobular. Moreover, the 3D 15N-NOESY HSQC spectrum exhibits few long-range NOEs. Similar spectral features have been observed for repeat modules in other polypeptides and are characteristic of an elongated conformation. The results provide a residue-specific description of a silk sequence in nonaqueous solution and may be insightful for understanding the fold and topology of highly concentrated, stable silk before spinning. Additionally, the insights obtained may find application in future design and large-scale production and storage of synthetic silks in organic solvents. PMID:19177364

  13. Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems.

    PubMed

    Adamczyk-Popławska, Monika; Kondrzycka, Aneta; Urbanek, Katarzyna; Piekarowicz, Andrzej

    2003-11-01

    All known type I restriction and modification (R-M) systems of Escherichia coli and Salmonella enterica belong to one of four discrete families: type IA, IB, IC or ID. The classification of type I systems from a wide range of other genera is mainly based on complementation and molecular evidence derived from the comparison of the amino acid similarity of the corresponding subunits. This affiliation was seldom based on the strictest requirement for membership of a family, which depends on relatedness as demonstrated by complementation tests. This paper presents data indicating that the type I NgoAV R-M system from Neisseria gonorrhoeae, despite the very high identity of HsdM and HsdR subunits with members of the type IC family, does not show complementation with E. coli type IC R-M systems. Sequence analysis of the HsdS subunit of several different potential type IC R-M systems shows that the presence of different tetra-amino-acid sequence repeats, e.g. TAEL, LEAT, SEAL, TSEL, is characteristic for type IC R-M systems encoded by distantly related bacteria. The other regions of the HsdS subunits potentially responsible for subunit interaction are also different between a group of distantly related bacteria, but show high similarity within these bacteria. Complementation between the NgoAV R-M system and members of the EcoR124 R-M family can be restored by changing the tetra-amino-acid repeat within the HsdS subunit. The authors propose that the type IC family of R-M systems could consist of several complementation subgroups whose specificity would depend on differences in the conserved regions of the HsdS polypeptide. PMID:14600243

  14. Association between the variable number of tandem repeat polymorphism in the third exon of the dopamine D4 receptor gene and sensitivity to analgesics and pain in patients undergoing painful cosmetic surgery.

    PubMed

    Aoki, Yoshinori; Nishizawa, Daisuke; Kasai, Shinya; Fukuda, Ken-Ichi; Ichinohe, Tatsuya; Yamashita, Shuichiro; Ikeda, Kazutaka

    2013-05-10

    To elucidate the mechanisms of individual differences in pain and analgesic sensitivity, we analyzed the variable number of tandem repeat polymorphism in the third exon of the dopamine D4 receptor gene. Alleles that were less than four repeats long and four or more repeats long were considered Short and Long, respectively. We found that the Short/Short genotype group was significantly more sensitive to pain and less sensitive to analgesics than the Short/Long+Long/Long genotype group. Our data suggest that this polymorphism may predict individual differences in pain and analgesic sensitivity and help achieve adequate pain control in the future. PMID:23458670

  15. Repeatability of gradient ultrahigh pressure liquid chromatography-tandem mass spectrometry methods in instrument-controlled thermal environments.

    PubMed

    Grinias, James P; Wong, Jenny-Marie T; Kennedy, Robert T

    2016-08-26

    The impact of viscous friction on eluent temperature and column efficiency in liquid chromatography is of renewed interest as the need for pressures exceeding 1000bar to use with columns packed with sub-2μm particles has grown. One way the development of axial and radial temperature gradients that arise due to viscous friction can be affected is by the thermal environment the column is placed in. In this study, a new column oven integrated into an ultrahigh pressure liquid chromatograph that enables both still-air and forced-air operating modes is investigated to find the magnitude of the effect of the axial thermal gradient that forms in 2.1×100mm columns packed with sub-2μm particles in these modes. Temperature increases of nearly 30K were observed when the generated power of the column exceeded 25W/m. The impact of the heating due to viscous friction on the repeatability of peak capacity, elution time, and peak area ratio to an internal standard for a gradient UHPLC-MS/MS method to analyze neurotransmitters was found to be limited. This result indicates that high speed UHPLC-MS/MS gradient methods under conditions of high viscous friction may be possible without the negative effects typically observed with isocratic separations under similar conditions. PMID:27457561

  16. Variable number of tandem repeat polymorphisms of DRD4: re-evaluation of selection hypothesis and analysis of association with schizophrenia

    PubMed Central

    Hattori, Eiji; Nakajima, Mizuho; Yamada, Kazuo; Iwayama, Yoshimi; Toyota, Tomoko; Saitou, Naruya; Yoshikawa, Takeo

    2009-01-01

    Associations have been reported between the variable number of tandem repeat (VNTR) polymorphisms in the exon 3 of dopamine D4 receptor gene gene and multiple psychiatric illnesses/traits. We examined the distribution of VNTR alleles of different length in a Japanese cohort and found that, as reported earlier, the size of allele ‘7R' was much rarer (0.5%) in Japanese than in Caucasian populations (∼20%). This presents a challenge to an earlier proposed hypothesis that positive selection favoring the allele 7R has contributed to its high frequency. To further address the issue of selection, we carried out sequencing of the VNTR region not only from human but also from chimpanzee samples, and made inference on the ancestral repeat motif and haplotype by use of a phylogenetic analysis program. The most common 4R variant was considered to be the ancestral haplotype as earlier proposed. However, in a gene tree of VNTR constructed on the basis of this inferred ancestral haplotype, the allele 7R had five descendent haplotypes in relatively long lineage, where genetic drift can have major influence. We also tested this length polymorphism for association with schizophrenia, studying two Japanese sample sets (one with 570 cases and 570 controls, and the other with 124 pedigrees). No evidence of association between the allele 7R and schizophrenia was found in any of the two data sets. Collectively, this study suggests that the VNTR variation does not have an effect large enough to cause either selection or a detectable association with schizophrenia in a study of samples of moderate size. PMID:19092778

  17. Genetic Diversity of Mycobacterium africanum Clinical Isolates Based on IS6110-Restriction Fragment Length Polymorphism Analysis, Spoligotyping, and Variable Number of Tandem DNA Repeats

    PubMed Central

    Viana-Niero, Cristina; Gutierrez, Cristina; Sola, Christophe; Filliol, Ingrid; Boulahbal, Fadila; Vincent, Véronique; Rastogi, Nalin

    2001-01-01

    A collection of 105 clinical isolates originally identified as Mycobacterium africanum were characterized using both phenotypic and genotyping methods. The phenotypic methods included routine determination of cultural properties and biochemical tests used to discriminate among the members of the M. tuberculosis complex, whereas genotypic characterization was based on IS6110-restriction fragment length polymorphism (IS6110-RFLP) analysis, IS1081-RFLP analysis, direct repeat-based spacer oligonucleotide typing (spoligotyping), variable number of tandem DNA repeats (VNTR), and the polymorphism of the oxyR, pncA, and mtp40 loci. The results obtained showed that a majority of M. africanum isolates were characterized by a specific spoligotyping pattern that was intermediate between those of M. tuberculosis and M. bovis, which do not hybridize with spacers 33 to 36 and spacers 39 to 43, respectively. A tentative M. africanum-specific spoligotyping signature appeared to be absence of spacers 8, 9, and 39. Based on spoligotyping, as well as the polymorphism of oxyR and pncA, a total of 24 isolates were excluded from the final study (19 were identified as M. tuberculosis, 2 were identified as M. canetti, and 3 were identified as M. bovis). The remaining 81 M. africanum isolates were efficiently subtyped in three distinct subtypes (A1 to A3) by IS6110-RFLP analysis and spoligotyping. The A1 and A2 subgroups were relatively more homogeneous upon spoligotyping than A3. Further analysis of the three subtypes by VNTR corroborated the highly homogeneous nature of the A2 subtype but showed significant variations for subtypes A1 and A3. A phylogenetic tree based on a selection of isolates representing the three subtypes using VNTR and spoligotyping alone or in combination confirmed the subtypes described as well as the heterogeneity of subtype A3. PMID:11136749

  18. Characterization of a novel spore wall protein NbSWP16 with proline-rich tandem repeats from Nosema bombycis (microsporidia).

    PubMed

    Wang, Ying; Dang, Xiaoqun; Ma, Qiang; Liu, Fangyan; Pan, Guoqing; Li, Tian; Zhou, Zeyang

    2015-04-01

    Nosema bombycis, a pathogen of silkworm pebrine, is an obligate unicellular eukaryotic parasite. It is reported that the spore wall proteins have essential functions in the adherence and infection process of microsporidia. To date, the information related to spore wall proteins from microsporidia is still limited. Here, a 44 kDa spore wall protein NbSWP16 was characterized in N. bombycis. In NbSWP16, a 25 amino acids signal peptide and 3 heparin binding motifs were predicted. Interestingly, a region that contains 3 proline-rich tandem repeats lacking homology to any known protein was also present in this protein. The immunofluorescence analysis (IFA) demonstrated that distinct fluorescent signals were detected both on the surface of mature spores and the germinated spore coats. Immunolocation by electron microscopy revealed that NbSWP16 localized on the exospore regions. Finally, spore adherence analysis indicated that spore adherence to host cell was decreased more than 20% by anti-NbSWP16 blocking compared with the negative control in vitro. In contrast with anti-NbSWP16, no remarkable decrement inhibition was detected when antibodies of NbSWP16 and NbSWP5 were used simultaneously. Collectively, these results suggest that NbSWP16 is a new exospore protein and probably be involved in spore adherence of N. bombycis. PMID:25363531

  19. An Empirical Comparison of Short Tandem Repeats (STRs) and Single Nucleotide Polymorphisms (SNPs) for Relatedness Estimation in Chinese Rhesus Macaques (Macaca mulatta)

    PubMed Central

    Ross, Cody T.; Weise, Jessica A.; Bonnar, Sarah; Nolin, David; Trask, Jessica Satkoski; Smith, David Glenn; Ferguson, Betsy; Ha, James; Kubisch, H. Michael; Vinson, Amanda; Kanthaswamy, Sree

    2015-01-01

    We compare the effectiveness of short tandem repeat (STR) and single nucleotide polymorphism (SNP) genotypes for estimating pairwise relatedness, using molecular data and pedigree records from a captive Chinese rhesus macaque population at the California National Primate Research Center. We find that a panel of 81 SNPs is as effective at estimating first-order kin relationships as a panel of 14 highly polymorphic STRs. We note, however, that the selected STRs provide more precise predictions of relatedness than the selected SNPs, and may be preferred in contexts that require the discrimination of kin related more distantly than first-order relatives. Additionally, we compare the performance of three commonly used relatedness estimation algorithms, and find that the Wang [2002] algorithm outperforms other algorithms when analyzing STR data, while the Queller and Goodnight [1994] algorithm outperforms other algorithms when analyzing SNP data. Future research is needed to address the number of SNPs required to reach the discriminatory power of a standard STR panel in relatedness estimation for primate colony management. PMID:24273109

  20. Evaluation and Selection of Multilocus Variable-Number Tandem-Repeat Analysis Primers for Genotyping Brucella abortus Biovar 1 Isolated from Human Patients

    PubMed Central

    Lee, Subok; Hwang, Kyu-Jam; Park, Mi-Yeoun; Hwang, Seon-Do; Chai, Hee-Youl; Chu, Hyuk; Park, Sang-Hee

    2013-01-01

    Objectives Brucellosis is the most common bacterial zoonosis in the world. Multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) is a molecular method for genotyping bacterial species. Brucella abortus biovar I was isolated from most of the brucellosis-suspected patients in Korea. This study was conducted to investigate the ability of various MLVA primers that are used for molecular typing B. abortus isolates and for analyzing their epidemiological data. Methods A total of 80 human isolates of B. abortus biovar I isolated from human patients and the reference strain were used for MLVA. Genetic diversity was determined by calculating the Simpson's diversity index (DI) of each VNTR locus. The Brucella strains were subcultured 30 times to determine the stability of each locus. The DNA of the strains cultivated in each passage was extracted and subjected to MLVA for further investigation. Results The 15 VNTR loci were selected based on high DI values. The DIs of the 15 VNTR loci showed considerable discrimination power ranging from 59% for Bruce 43 to 87% for Bruce 22. Bruce 09, Bruce 11, Bruce 16, Bruce 42, and Bruce 43 were confirmed to remain stable in vitro among the 15 VNTR loci selected. Conclusion The results of this study suggest that the five loci subsets may be a useful epidemiological tool for investigating B. abortus biovar 1 outbreak. PMID:24298442

  1. Investigation of Clostridium difficile interspecies relatedness using multilocus sequence typing, multilocus variable-number tandem-repeat analysis and antimicrobial susceptibility testing.

    PubMed

    Rodriguez, C; Avesani, V; Taminiau, B; Van Broeck, J; Brévers, B; Delmée, M; Daube, G

    2015-12-01

    Multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA) and antimicrobial susceptibility were performed on 37 animal and human C. difficile isolates belonging to 15 different PCR-ribotypes in order to investigate the relatedness of human and animal isolates and to identify possible transmission routes. MLVA identified a total of 21 different types while MLST only distinguished 12 types. Identical C. difficile strains were detected in the same animal species for PCR-ribotypes 014, 078, UCL 16U and UCL 36, irrespective of their origin or the isolation date. Non clonal strains were found among different hosts; however, a high genetic association between pig and cattle isolates belonging to PCR-ribotype 078 was revealed. MLVA also showed genetic differences that clearly distinguished human from animal strains. For a given PCR-ribotype, human and animal strains presented a similar susceptibility to the antimicrobials tested. All strains were susceptible to vancomycin, metronidazole, chloramphenicol and rifampicin, while PCR-ribotypes 078, UCL 5a, UCL 36 and UCL 103 were associated with erythromycin resistance. The data suggest a wide dissemination of clones at hospitals and breeding-farms or a contamination at the slaughterhouse, but less probability of interspecies transmission. However, further highly discriminatory genotyping methods are necessary to elucidate interspecies and zoonotic transmission of C. difficile. PMID:26545846

  2. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

    PubMed

    Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

    2016-09-01

    The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates. PMID:27352221

  3. Multilocus variable-number tandem-repeat analysis and multilocus sequence typing reveal genetic relationships among Clostridium difficile isolates genotyped by restriction endonuclease analysis.

    PubMed

    Marsh, Jane W; O'Leary, Mary M; Shutt, Kathleen A; Sambol, Susan P; Johnson, Stuart; Gerding, Dale N; Harrison, Lee H

    2010-02-01

    Numbers of Clostridium difficile infections have increased worldwide in the past decade. While infection with C. difficile remains predominantly a health care-associated infection, there may also be an increased incidence of community-associated infections. C. difficile strains of public health significance continue to emerge, and reliable genotyping methods for epidemiological investigations and global surveillance of C. difficile are required. In this study, multilocus sequence typing (MLST) and multilocus variable-number tandem-repeat analysis (MLVA) were performed on a set of 157 spatially and temporally diverse C. difficile isolates that had been previously genotyped by restriction endonuclease analysis (REA) to determine the concordance among these genotyping methods. In addition, sequence analysis of the tcdC genotype was performed to investigate the association of allelic variants with epidemic C. difficile isolates. Overall, the MLST and MLVA data were concordant with REA genotyping data. MLST was less discriminatory than either MLVA or REA, yet this method established C. difficile genetic lineage. MLVA was highly discriminatory and demonstrated relationships among the MLST genetic lineages and REA genotypes that were previously unrecognized. Several tcdC genotypes were specific to epidemic clones, highlighting the possible importance of toxin misregulation in C. difficile disease pathogenesis. This study demonstrates that a combination of MLST and MLVA may prove useful for the investigation and surveillance of emergent C. difficile clones of global public health concern. PMID:19955268

  4. A multiple-locus variable-number tandem repeat analysis (MLVA) of Listeria monocytogenes isolated from Norwegian salmon-processing factories and from listeriosis patients.

    PubMed

    Lunestad, B T; Truong, T T T; Lindstedt, B-A

    2013-10-01

    The objective of this study was to characterize Listeria monocytogenes isolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65 L. monocytogenes isolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients. L. monocytogenes with this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis. PMID:23218175

  5. Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina

    PubMed Central

    Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

    2014-01-01

    Aim To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. Methods This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Results Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Conclusion Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other. PMID:25358886

  6. Towards Improvements in the Estimation of the Coalescent: Implications for the Most Effective Use of Y Chromosome Short Tandem Repeat Mutation Rates

    PubMed Central

    Bird, Steven C.

    2012-01-01

    Over the past two decades, many short tandem repeat (STR) microsatellite loci on the human Y chromosome have been identified together with mutation rate estimates for the individual loci. These have been used to estimate the coalescent age, or the time to the most recent common ancestor (TMRCA) expressed in generations, in conjunction with the average square difference measure (ASD), an unbiased point estimator of TMRCA based upon the average within-locus allele variance between haplotypes. The ASD estimator, in turn, depends on accurate mutation rate estimates to be able to produce good approximations of the coalescent age of a sample. Here, a comparison is made between three published sets of per locus mutation rate estimates as they are applied to the calculation of the coalescent age for real and simulated population samples. A novel evaluation method is developed for estimating the degree of conformity of any Y chromosome STR locus of interest to the strict stepwise mutation model and specific recommendations are made regarding the suitability of thirty-two commonly used Y-STR loci for the purpose of estimating the coalescent. The use of the geometric mean for averaging ASD and across loci is shown to improve the consistency of the resulting estimates, with decreased sensitivity to outliers and to the number of STR loci compared or the particular set of mutation rates selected. PMID:23119076

  7. Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot.

    PubMed

    N'guessan, Carine Aya; Brisse, Sylvain; Le Roux-Nio, Anne-Claire; Poussier, Stéphane; Koné, Daouda; Wicker, Emmanuel

    2013-03-01

    Ralstonia solanacearum is an important soil borne bacterial plant pathogen causing bacterial wilt on many important crops. To better monitor epidemics, efficient tools that can identify and discriminate populations are needed. In this study, we assessed variable number of tandem repeats (VNTR) genotyping as a new tool for epidemiological surveillance of R. solanacearum phylotypes, and more specifically for the monitoring of the monomorphic ecotypes "Moko" (banana-pathogenic) and "brown rot" (potato-pathogenic under cool conditions). Screening of six R. solanacearum genome sequences lead to select 36 VNTR loci that were preliminarily amplified on 24 strains. From this step, 26 single-locus primer pairs were multiplexed, and applied to a worldwide collection of 337 strains encompassing the whole phylogenetic diversity, with revelation on a capillary-electrophoresis genotype. Four loci were monomorphic within all phylotypes and were not retained; the other loci were highly polymorphic but displayed a clear phylotype-specificity. Phylotype-specific MLVA schemes were thus defined, based on 13 loci for phylotype I, 12 loci for phylotype II, 11 loci for phylotype III and 6 for phylotype IV. MLVA typing was significantly more discriminative than egl-based sequevar typing, particularly on monomorphic "brown rot" ecotype (phylotype IIB/sequevar 1) and "Moko disease" clade 4 (Phylotype IIB/sequevar 4). Our results raise promising prospects for studies of population genetic structures and epidemiological monitoring. PMID:23376194

  8. Characterization of Genetic Diversity of Bacillus anthracis in France by Using High-Resolution Melting Assays and Multilocus Variable-Number Tandem-Repeat Analysis ▿ †

    PubMed Central

    Derzelle, S.; Laroche, S.; Le Flèche, P.; Hauck, Y.; Thierry, S.; Vergnaud, G.; Madani, N.

    2011-01-01

    Using high-resolution melting (HRM) analysis, we developed a cost-effective method to genotype a set of 13 phylogenetically informative single-nucleotide polymorphisms (SNPs) within the genome of Bacillus anthracis. SNP discrimination assays were performed in monoplex or duplex and applied to 100 B. anthracis isolates collected in France from 1953 to 2009 and a few reference strains. HRM provided a reliable and cheap alternative to subtype B. anthracis into one of the 12 major sublineages or subgroups. All strains could be correctly positioned on the canonical SNP (canSNP) phylogenetic tree, except the divergent Pasteur vaccine strain ATCC 4229. We detected the cooccurrence of three canSNP subgroups in France. The dominant B.Br.CNEVA sublineage was found to be prevalent in the Alps, the Pyrenees, the Auvergne region, and the Saône-et-Loire department. Strains affiliated with the A.Br.008/009 subgroup were observed throughout most of the country. The minor A.Br.001/002 subgroup was restricted to northeastern France. Multiple-locus variable-number tandem-repeat analysis using 24 markers further resolved French strains into 60 unique profiles and identified some regional patterns. Diversity found within the A.Br.008/009 and B.Br.CNEVA subgroups suggests that these represent old, ecologically established clades in France. Phylogenetic relationships with strains from other parts of the world are discussed. PMID:21998431

  9. Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1.

    PubMed

    Rashid, Mahamud-Ur; Almeida, Mathieu; Azman, Andrew S; Lindsay, Brianna R; Sack, David A; Colwell, Rita R; Huq, Anwar; Morris, J Glenn; Alam, Munirul; Stine, O Colin

    2016-06-01

    Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10(-6)) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC. PMID:27190166

  10. Forensic and population genetic analysis of Xinjiang Uyghur population on 21 short tandem repeat loci of 6-dye GlobalFiler™ PCR Amplification kit.

    PubMed

    Zhang, Honghua; Xia, Mingying; Qi, Lijie; Dong, Lei; Song, Shuang; Ma, Teng; Yang, Shuping; Jin, Li; Li, Liming; Li, Shilin

    2016-05-01

    Estimating the allele frequencies and forensic statistical parameters of commonly used short tandem repeat (STR) loci of the Uyghur population, which is the fifth largest group in China, provides a more precise reference database for forensic investigation. The 6-dye GlobalFiler™ Express PCR Amplification kit incorporates 21 autosomal STRs, which have been proven that could provide reliable DNA typing results and enhance the power of discrimination. Here we analyzed the GlobalFiler STR loci on 1962 unrelated individuals from Chinese Uyghur population of Xinjiang, China. No significant deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were detected within and between the GlobalFiler STR loci. SE33 showed the greatest power of discrimination in Uyghur population, whereas TPOX showed the lowest. The combined power of discrimination was 99.999999999999999999999998746%. No significant difference was observed between Uyghur and the other two Uyghur populations at all tested STRs, as well as Dai and Mongolian. Significant differences were only observed between Uyghur and other Chinese populations at TH01, as well as Central-South Asian at D13S317, East Asian at TH01 and VWA. The phylogenetic analysis showed that Uyghur is genetically close to Chinese populations, as well as East Asian and Central-South Asian. PMID:26809046

  11. Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System

    PubMed Central

    Essakhi, Salwa; Cesbron, Sophie; Fischer-Le Saux, Marion; Bonneau, Sophie; Jacques, Marie-Agnès

    2015-01-01

    Xanthomonas arboricola is conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed that X. arboricola also encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess the X. arboricola population structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100 X. arboricola strains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection of X. arboricola strains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containing Xanthomonas arboricola pv. juglandis strains. Some nonpathogenic strains of X. arboricola did not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity in X. arboricola. T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity in X. arboricola. PMID:26048944

  12. Use of a multilocus variable-number tandem repeat analysis method for molecular subtyping and phylogenetic analysis of Neisseria meningitidis isolates

    PubMed Central

    Liao, Jui-Cheng; Li, Chun-Chin; Chiou, Chien-Shun

    2006-01-01

    Background The multilocus variable-number tandem repeat (VNTR) analysis (MLVA) technique has been developed for fine typing of many bacterial species. The genomic sequences of Neisseria meningitidis strains Z2491, MC58 and FAM18 have been available for searching potential VNTR loci by computer software. In this study, we developed and evaluated a MLVA method for molecular subtyping and phylogenetic analysis of N. meningitidis strains. Results A total of 12 VNTR loci were identified for subtyping and phylogenetic analysis of 100 N. meningitidis isolates, which had previously been characterized by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. The number of alleles ranges from 3 to 40 for the 12 VNTR loci; theoretically, the numbers of alleles can generate more than 5 × 1011 MLVA types. In total, 93 MLVA types were identified in the 100 isolates, indicating that MLVA is powerful in discriminating N. meningitidis strains. In phylogenetic analysis with the minimal spanning tree method, clonal relationships, established with MLVA types, agreed well with those built with ST types. Conclusion Our study indicates that the MLVA method has a higher degree of resolution than PFGE in discriminating N. meningitidis isolates and may be a useful tool for phylogenetic studies of strains evolving over different time scales. PMID:16686962

  13. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians.

    PubMed

    Budowle, B; Moretti, T R; Baumstark, A L; Defenbaugh, D A; Keys, K M

    1999-11-01

    Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group. PMID:10582369

  14. Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1

    PubMed Central

    Rashid, Mahamud-ur; Almeida, Mathieu; Azman, Andrew S.; Lindsay, Brianna R.; Sack, David A.; Colwell, Rita R.; Huq, Anwar; Morris, J. Glenn; Alam, Munirul; Stine, O. Colin

    2016-01-01

    Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10−6) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC. PMID:27190166

  15. Phylogenetic analysis of encapsulated and non-encapsulated Trichinella species by studying the 5S rDNA tandemly repeated intergenic region.

    PubMed

    van der Giessen, J W B; Fonville, M; Briels, I; Pozio, E

    2005-09-01

    The identification of sequence regions in the genomes of pathogens which can be useful to distinguish among species and genotypes, is of great importance for epidemiological, molecular, and phylogenetic studies. The 5S ribosomal DNA intergenic spacer region has been identified as a good target to distinguish among eight Trichinella species and genotypes. The recent discovery of two non-encapsulated species in this genus, Trichinella papuae and Trichinella zimbabwensis, which can infect both mammals and reptiles, has suggested analyzing their 5S rDNA. Amplification of the tandem repeats of the 5S rDNA intergenic region of encapsulated species of Trichinella shows a 751bp fragment, whereas the three non-encapsulated species show a fragment of 800bp with T. pseudospiralis showing an additional fragment of 522bp. Although the size of the 800bp PCR fragments of T. papuae and T. zimbabwensis are similar to that of T. pseudospiralis, there are differences in the 5S rDNA intergenic regions among the three non-encapsulated species. Phylogenetic analysis of the 5S rDNA intergenic regions shows a clustering together of the three non-encapsulated Trichinella species that is well separated from the encapsulated ones. In addition, a single PCR-based method allows distinguishing non-encapsulated and encapsulated species. PMID:16076532

  16. Genetic Diversity of Neisseria meningitidis Serogroup C ST-4821 in China Based on Multiple-Locus Variable Number Tandem Repeat Analysis

    PubMed Central

    Shan, Xiaoying; Zhang, Ji; Zhou, Haijian; Zhu, Bingqing; Xu, Li; Shao, Zhujun; Jiang, Baofa

    2014-01-01

    Neisseria meningitidis sequence type (ST)-4821 was first reported in China in 2003, and a new hyper-virulent lineage has been designated as the ST-4821 complex. A large number of N. meningitidis ST-4821 strains have been identified in China since 2003; however, the microevolution characteristics of this complex are unclear. Different combinations of variable number of tandem repeats (VNTR) loci were used in multiple-locus VNTR analysis (MLVA) to analyze 118 N. meningitidis serogroup C ST-4821 strains isolated from seventeen provinces between 2003 and 2012. Additionally, MLVA with five VNTR loci was performed due to its high discriminatory power. One hundred and eighteen isolates were found to comprise 112 subtypes based on MLVA, and 16 outbreak-associated strains were clustered into one group. These data indicate a high level of diversity for N. meningitidis ST-4821 due to microevolution in the last decade. In addition, the results revealed high similarity between isolates from the same geographic origins, which is helpful when monitoring the spread of N. meningitidis serogroup C ST-4821 and will provide valuable information for the control and prevention of bacterial meningitis in China. PMID:25375168

  17. Evidence of tandem repeat and extra thiol-groups resulted in the polymeric formation of bovine haptoglobin: a unique structure of Hp 2-2 phenotype.

    PubMed

    Lai, Yi An; Lai, I Hsiang; Tseng, Chi Feng; Lee, James; Mao, Simon J T

    2007-11-30

    Human plasma Hp is classified as 1-1, 2-1, and 2-2. They are inherited from two alleles Hp 1 and Hp 2, but there is only Hp 1 in almost all the animal species. Hp 2-2 molecule is extremely large and heterogeneous associated with the development of inflammatory-related diseases. In this study, we expressed entire bovine Hp in E. coli as a alphabeta linear form. Interestingly, the antibodies prepared against this form could recognize the subunit of native Hp. In stead of a complicated column method, the antibody was able to isolate bovine Hp via immunoaffinity and gel-filtration columns. The isolated Hp is polymeric containing two major molecular forms (660 and 730 kDa). Their size and hemoglobin binding complex are significantly larger than that of human Hp 2-2. The amino-acid sequence deducted from the nucleotide sequence is similar to human Hp 2 containing a tandem repeat over the alpha chain. Thus, the Hp 2 allele is not unique in human. We also found that there is one additional -SH group (Cys-97) in bovine alpha chain with a total of 8 -SH groups, which may be responsible for the overall polymeric structure that is markedly different from human Hp 2-2. The significance of the finding and its relationship to structural evolution are also discussed. PMID:18047801

  18. Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA).

    PubMed

    Bergonier, Dominique; Sobral, Daniel; Feßler, Andrea T; Jacquet, Eric; Gilbert, Florence B; Schwarz, Stefan; Treilles, Michaël; Bouloc, Philippe; Pourcel, Christine; Vergnaud, Gilles

    2014-01-01

    Staphylococcus aureus is one of the main etiological agents of mastitis in ruminants. In the present retrospective study, we evaluated the potential interest of a previously described automated multiple loci Variable Number of Tandem Repeats (VNTR) Assay (MLVA) comprising 16 loci as a first line tool to investigate the population structure of S. aureus from mastitis. We determined the genetic diversity of S. aureus strains from cases of clinical and subclinical mastitis in dairy cattle (n = 118, of which 16 were methicillin-resistant), sheep (n = 18) and goats (n = 16). The 152 strains could be subdivided into 115 MLVA genotypes (including 14 genotypes for the ovine strains and 15 genotypes for the caprine strains). This corresponds to a discriminatory index (D) value of 0.9936. Comparison with published MLVA data obtained using the same protocol applied to strains from diverse human and animal origins revealed a low number (8.5%) of human-related MLVA genotypes among the present collection. Eighteen percent of the S. aureus mastitis collection belonged to clonal complexes apparently not associated with other pathological conditions. Some of them displayed a relatively low level of diversity in agreement with a restricted ecological niche. These findings provide arguments suggesting that specific S. aureus lineages particularly adapted to ruminant mammary glands have emerged and that MLVA is a convenient tool to provide a broad overview of the population, owing to the availability via internet of databases compiling published MLVA genotypes. PMID:25315988

  19. Oral Administration of Recombinant Lactococcus lactis Expressing HSP65 and Tandemly Repeated P277 Reduces the Incidence of Type I Diabetes in Non-Obese Diabetic Mice

    PubMed Central

    Ma, Yanjun; Liu, Jingjing; Hou, Jing; Dong, Yuankai; Lu, Yong; Jin, Liang; Cao, Rongyue; Li, Taiming; Wu, Jie

    2014-01-01

    Diabetes mellitus type 1 (DM1) is an autoimmune disease that gradually destroys insulin-producing beta-cells. We have previously reported that mucosal administration of fusion protein of HSP65 with tandem repeats of P277 (HSP65-6P277) can reduce the onset of DM1 in non-obese diabetic (NOD) mice. To deliver large amounts of the fusion protein and to enhance long-term immune tolerance effects, in the present study, we investigated the efficacy of using orally administrated L. lactis expressing HSP65-6P277 to reduce the incidence of DM1 in NOD mice. L. lactis strain NZ9000 was engineered to express HSP65-6P277 either constitutively or by nisin induction. After immunization via gavage with the recombinant L. lactis strains to groups of 4-week old female NOD mice for 36 weeks, we observed that oral administration of recombinant L. Lactis resulted in the prevention of hyperglycemia, improved glucose tolerance and reduced insulitis. Immunologic analysis showed that treatment with recombinant L. lactis induced HSP65- and P277- specific T cell immuno-tolerance, as well as antigen-specific proliferation of splenocytes. The results revealed that the DM1-preventing function was in part caused by a reduction in the pro-inflammatory cytokine IFN-γ and an increase in the anti-inflammatory cytokine IL-10. Orally administered recombinant L. lactis delivering HSP65-6P277 may be an effective therapeutic approach in preventing DM1. PMID:25157497

  20. Virulence Gene Profile and Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) of Enteroinvasive Escherichia coli (EIEC) Isolates From Patients With Diarrhea in Kerman, Iran

    PubMed Central

    Hosseini Nave, Hossein; Mansouri, Shahla; Taati Moghadam, Majid; Moradi, Mohammad

    2016-01-01

    Background Enteroinvasive Escherichia coli (EIEC) isolates cause dysentery in humans. Several virulence factors associated with EIEC pathogenesis have been characterized. Multilocus variable-number tandem-repeat analysis (MLVA) is a PCR-based method that has been used for genotyping bacterial pathogens. Objectives The aim of this study was to investigate the distribution of virulence factor genes in EIEC isolates from patients with diarrhea in Kerman, Iran, as well as the genetic relationships between these isolates. Patients and Methods A total of 620 diarrheic stool samples were collected from patients attending two hospitals in Kerman from June 2013 to August 2014. All isolates were confirmed as EIEC by PCR for the ipaH gene. The EIEC isolates were evaluated by PCR for the presence of nine virulence genes (ial, set1A, sen, virF, invE, sat, sigA, pic, and sepA). MLVA was performed for all EIEC isolates. Results A total of 11 EIEC isolates were identified, and all were positive for the ial gene. The invE and virF genes were observed in 81.8% of the isolates, while sen, sigA, and pic were detected in 72.7%, 63.6%, and 27.3% of the isolates, respectively. None of the isolates were positive for the sat, set, and sepA genes. Using MLVA, the 11 total isolates were divided into five types. Conclusions By studying the profiles of virulence genes and MLVA, it can be concluded that EIEC isolates do not have high heterogeneity and are derived from a limited number of clones.

  1. Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide

    PubMed Central

    Ciarroni, Serena; Gallipoli, Lorenzo; Taratufolo, Maria C.; Butler, Margi I.; Poulter, Russell T. M.; Pourcel, Christine; Vergnaud, Gilles; Balestra, Giorgio M.; Mazzaglia, Angelo

    2015-01-01

    The bacterial canker of kiwifruit by Pseudomonas syringae pv. actinidiae is an emblematic example of a catastrophic disease of fruit crops. In 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many Actinidia spp. orchards all over the world. In order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with previous records. In this report a worldwide collection of 142 strains was analyzed by MLVA, chosen as investigative technique for its efficacy, reproducibility, simplicity and low cost. A panel of 13 Variable Number of Tandem Repeats (VNTR) loci was identified and used to describe the pathogen population. The MLVA clustering is highly congruent with the population structure as previously established by other molecular approaches including whole genome sequencing and correlates with geographic origin, time of isolation and virulence. For convenience, we divided the VNTR loci in two panels. Panel 1 assay, using six loci, recognizes 23 different haplotypes, clustered into ten complexes with highest congruence with previous classifications. Panel 2, with seven VNTR loci, provides discriminatory power. Using the total set of 13 VNTR loci, 58 haplotypes can be distinguished. The recent hypervirulent type shows very limited diversity and includes, beside the strains from Europe, New Zealand and Chile, a few strains from Shaanxi, China. A broad genetic variability is observed in China, but different types are also retrievable in Japan and Korea. The low virulent strains cluster together and are very different from the other MLVA genotypes. Data were used to generate a public database in MLVAbank. MLVA represents a very promising first-line assay for large-scale routine genotyping, prior to whole genome sequencing of only the most relevant samples. PMID:26262683

  2. Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of "Mycobacterium avium subsp. hominissuis" with Establishment of a PCR Database.

    PubMed

    Iakhiaeva, Elena; Howard, Susan T; Brown Elliott, Barbara A; McNulty, Steven; Newman, Kristopher L; Falkinham, Joseph O; Williams, Myra; Kwait, Rebecca; Lande, Leah; Vasireddy, Ravikiran; Turenne, Christine; Wallace, Richard J

    2016-04-01

    "Mycobacterium aviumsubsp.hominissuis" is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilmM. aviumisolates underwent molecular identification. Testing for IS901was done to separateM. aviumsubsp.aviumfromM. aviumsubsp.hominissuis VNTR types were defined using VNTR loci, and subtyping was performed using 3'hsp65and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes ofM. aviumsubsp.hominissuis(IS901negative) were identified among 416 isolates ofM. aviumfrom 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included ≥4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3'hsp65sequence code (sequevar). A total of 44 isolates belonging to fourM. aviumsubsp.hominissuisVNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901PCR primers. By sequencing, all 44 amplicons were not IS901but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis ofM. aviumsubsp.hominissuisisolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates ofM. aviumsubsp.aviumwere identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan. PMID:26739155

  3. Utilizing Rapid Multiple-Locus Variable-Number Tandem-Repeat Analysis Typing To Aid Control of Hospital-Acquired Clostridium difficile Infection: a Multicenter Study

    PubMed Central

    Manzoor, Susan; Marriott, Claire; Parsons, Helen; Waddington, Claire; Gossain, Savita; Szczepura, Ala; Stallard, Nigel; Hawkey, Peter M.

    2012-01-01

    The early identification of outbreaks is crucial for the control of Clostridium difficile infection. This study aimed to determine if the number of hospital-acquired C. difficile infections could be reduced by rapidly typing C. difficile strains using multiple-locus variable-number tandem-repeat analysis (MLVA) compared to typing using PCR ribotyping. A total of 16 hospitals were recruited to the study, and all periods of increased incidence (PIIs) of C. difficile infection were identified. The hospitals were randomized into two study arms, the test and the control, with all isolates typed in the test using MLVA and in the control using PCR ribotyping. Following a PII, each hospital received a structured questionnaire regarding control measures implemented or stopped prior to or following the typing results. During the study period, there were a total of 1,682 hospital-apportioned C. difficile toxin-positive cases, with 868 in the control and 814 in the test, with modeling demonstrating no differences between the two arms. A total of 245 PIIs occurred, involving 785 patients. There was a significant difference in the mean turnaround time between the ribotyping and MLVA typing (13.6 and 5.3 days, respectively [P < 0.001]). The discriminatory ability of MLVA was greater than ribotyping, with 85 outbreaks being confirmed by ribotyping and 62 by MLVA. In the test arm, 40.6% of respondents strongly agreed that the typing result had aided their management of clusters, as opposed to 9.9% in the control. The study demonstrated the utility of rapidly typing C. difficile strains, demonstrating that it aided the management of clusters, enabling effective targeting of infection control resources. PMID:22837319

  4. Evidence for human meiotic recombination interference obtained through construction of a short tandem repeat-polymorphism linkage map of chromosome 19

    SciTech Connect

    Weber, J.L.; Wang, Z.; Hansen, K.; Stephenson, M.; Kappel, C.; Salzman, S.; Wilkie, P.J. ); Keats, B. ); Dracopoli, N.C. ); Brandriff, B.F.; Olsen, A.S. )

    1993-11-01

    An improved linkage map for human chromosome 19 containing 35 short tandem repeat polymorphisms (STRPs) and one VNTR (D19S20) was constructed. The map included 12 new (GATA)[sub n] tetranucleotide STRPs. Although total lengths of the male (114 cM) and female (128 cM) maps were similar, at both ends of the chromosome male recombination exceeded female recombination, while in the interior portion of the map female recombination was in excess. Cosmid clones containing the STRP sequences were identified and were positioned along the chromosome by fluorescent in situ hybridization. Four rounds of careful checking and removal of genotyping errors allowed biologically relevant conclusions to be made concerning the numbers and distributions of recombination events on chromosome 19. The average numbers of recombinations per chromosome matched closely the lengths of the genetic maps computed by using the program CRIMAP. Significant numbers of chromosomes with zero, one, two, or three recombinations were detected as products of both female and male meioses. On the basis of the total number of observed pairs of recombination events in which only a single informative marker was situated between the two recombinations, a maximal estimate for the rate of meiotic STRP [open quotes]gene[close quotes] conversion without recombination was calculated as 3 [times] 10[sup [minus]4]/meiosis. For distances up to 30 cM between recombinations, many fewer chromosomes which had undergone exactly two recombinations were observed than were expected on the basis of the assumption of independent recombination locations. This strong new evidence for human meiotic interference will help to improve the accuracy of interpretation of clinical DNA test results involving polymorphisms flanking a genetic abnormality. 61 refs., 2 figs., 5 tabs.

  5. Variable-number tandem-repeat analysis of leptospiral DNA isolated from canine urine samples molecularly confirmed to contain pathogenic leptospires.

    PubMed

    Harkin, Kenneth R; Hays, Michael P

    2016-08-15

    OBJECTIVE To use variable-number tandem-repeat (VNTR) analysis to determine the infecting serovar and strain for leptospiral DNA isolated from canine urine samples confirmed through PCR testing to contain pathogenic leptospires and to evaluate the sensitivity and specificity of microscopic agglutination testing (MAT) for identifying the infecting serogroup. DESIGN Diagnostic survey and test evaluation. SAMPLE Leptospiral DNA isolated from urine samples from 98 dogs confirmed through PCR testing to have pathogenic leptospires in their urine. PROCEDURES VNTR analysis of DNA isolates was performed to identify the infecting leptospiral serovar and strain by use of primer pairs for the loci 4, 7, 10, and Lb5. Eighteen pathogenic and 2 saprophytic leptospiral serovars were used as reference strains for VNTR analysis. Results of MAT were compared with those of the PCR assay and VNTR analysis to determine the sensitivity and specificity of MAT for diagnosing leptospirosis and identifying the infecting serovar at various reciprocal titers. RESULTS VNTR analysis identified Leptospira kirschneri serovar Grippotyphosa strain DF as the most common infecting serovar in dogs (78/98 [80%]). Thirteen unique VNTR patterns could not be identified by comparison with the Leptospira reference strains used. The MAT had a maximum sensitivity of 41% and a specificity of 100% for identifying Grippotyphosa as the infecting serogroup. CONCLUSIONS AND CLINICAL RELEVANCE Findings confirmed the importance of Leptospira serovar Grippotyphosa among dogs in the United States. Serologic testing had poor sensitivity for identifying the infecting serogroup, and conclusions about emerging serogroups should be cautiously interpreted when serologic data are reported. PMID:27479284

  6. Multiple-locus variable-number tandem repeat analysis of Leptospira interrogans and Leptospira borgpetersenii isolated from small feral and wild mammals in East Asia.

    PubMed

    Koizumi, Nobuo; Izumiya, Hidemasa; Mu, Jung-Jung; Arent, Zbigniew; Okano, Shou; Nakajima, Chie; Suzuki, Yasuhiko; Mizutani Muto, Maki; Tanikawa, Tsutomu; Taylor, Kyle R; Komatsu, Noriyuki; Yoshimatsu, Kumiko; Thi Thu Ha, Hoang; Ohnishi, Makoto

    2015-12-01

    Leptospira spp. are the causative agents of a worldwide zoonosis, leptospirosis, maintained by various mammals. Each Leptospira serovar is frequently associated with a particular maintenance host, and recently, Leptospira genotype-host association has also been suggested to limit serovars to restricted areas. We investigated the molecular characteristics of L. interrogans and L. borgpetersenii which were isolated from small feral and wild animals in four East Asian states using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA using 11 loci was performed on 110 L. interrogans serogroups from Japan (79 strains of 5 serogroups from 3 animal species), Philippines (21; 3; 2), Taiwan (7; 2; 3), and Vietnam (3; 1; 1). A MLVA method using 4 loci for L. borgpetersenii was established and performed on 52 isolates from Japan (26; 3; 7), Philippines (13; 1; 2), and Taiwan (13; 1; 3). In L. interrogans, serogroups Autumnalis and Hebdomadis appeared more genetically diverse than serogroups Bataviae, Grippotyphosa, Icterohaemorrhagiae, Pomona, or Pyrogenes. The former serogroup strains with the exception of one Hebdomadis strain were isolated from Apodemus speciosus while all the latter serogroup strains with the exception of Grippotyphosa were isolated from Rattus norvegicus. L. borgpetersenii was isolated from at least 11 animal species while L. interrogans was isolated from five species, which might suggest a wider host range for L. borgpetersenii. Broad host preference in a single genotype was also observed, which colonized not only different species of the same genera but also multiple animal genera. This study demonstrates that there may be variability in the range of genetic diversity among different Leptospira serogroups, which may be attributed to maintenance host animals and environmental factors. PMID:26296603

  7. Evaluation of a Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Typing Human Brucella Isolates in a Region of Brucellosis Endemicity▿ †

    PubMed Central

    Kattar, Mireille M.; Jaafar, Rola F.; Araj, George F.; Le Flèche, Philippe; Matar, Ghassan M.; Abi Rached, Roland; Khalife, Simon; Vergnaud, Gilles

    2008-01-01

    Brucellosis remains an important anthropozoonosis worldwide. Brucella species are genetically homogeneous, and thus, the typing of Brucella species for epidemiological purposes by conventional molecular typing methods has remained elusive. Although many methods could segregate isolates into the phylogenetically recognized taxa, limited within-species genetic diversity has been identified. Recently, multilocus variable-number tandem-repeat analysis (MLVA) was found to have a high degree of resolution when it was applied to collections of Brucella isolates from geographically widespread locations, and an assay comprising 16 such loci (MLVA-16) was proposed. This scheme includes eight minisatellite loci (panel 1) and eight microsatellites (panel 2, which is subdivided into panels 2A and 2B). The utility of MLVA-16 for the subtyping of human Brucella isolates from geographically restricted regions needs to be further evaluated, and genotyping databases with worldwide coverage must be progressively established. In the present study, MLVA-16 was applied to the typing of 42 human Brucella isolates obtained from 41 patients recovered from 2002 to 2006 at a tertiary-care center in Lebanon. All isolates were identified as Brucella melitensis by MLVA-16 and were found to be closely related to B. melitensis isolates from neighboring countries in the Middle East when their genotypes were queried against those in the web-based Brucella2007 MLVA database (http://mlva.u-psud.fr/). Panel 2B, which comprised the most variable loci, displayed a very high discriminatory power, while panels 1 and 2A showed limited diversity. The most frequent genotype comprised seven isolates obtained over 7 weeks in 2002, demonstrating an outbreak from a common source. Two isolates obtained from one patient 5 months apart comprised another genotype, indicating relapsing disease. These findings confirm that MLVA-16 has a good discriminatory power for species determination, typing of B. melitensis

  8. Genetic stability of Brucella abortus isolates from an outbreak by multiple-locus variable-number tandem repeat analysis (MLVA16)

    PubMed Central

    2014-01-01

    Background Brucellosis caused by Brucella abortus is one of the most important zoonoses in the world. Multiple-locus variable-number tandem repeat analysis (MLVA16) has been shown be a useful tool to epidemiological traceback studies in B. abortus infection. Thus, the present study aimed (i) to evaluate the genetic diversity of B. abortus isolates from a brucellosis outbreak, and (ii) to investigate the in vivo stability of the MLVA16 markers. Results Three-hundred and seventy-five clinical samples, including 275 vaginal swabs and 100 milk samples, were cultured from a brucellosis outbreak in a cattle herd, which adopted RB51 vaccination and test-and-slaughter policies. Thirty-seven B. abortus isolates were obtained, eight from milk and twenty-nine from post-partum/abortion vaginal swabs, which were submitted to biotyping and genotyping by MLVA16. Twelve B. abortus isolates obtained from vaginal swabs were identified as RB51. Twenty four isolates, seven obtained from milk samples and seventeen from vaginal swabs, were identified as B. abortus biovar 3, while one isolate from vaginal swabs was identified as B. abortus biovar 1. Three distinct genotypes were observed during the brucellosis outbreak: RB observed in all isolates identified as RB51; W observed in all B. abortus biovar 3 isolates; and Z observed in the single B. abortus biovar 1 isolate. Epidemiological and molecular data show that the B. abortus biovar 1 genotype Z strain is not related to the B. abortus biovar 3 genotype W isolates, and represents a new introduction B. abortus during the outbreak. Conclusions The results of the present study on typing of multiple clinical B. abortus isolates from the same outbreak over a sixteen month period indicate the in vivo stability of MLVA16 markers, a low genetic diversity among B. abortus isolates and the usefulness of MLVA16 for epidemiological studies of bovine brucellosis. PMID:25015840

  9. Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping.

    PubMed

    Kim, Yong Tae; Lee, Dohwan; Heo, Hyun Young; Sim, Jeong Eun; Woo, Kwang Man; Kim, Do Hyun; Im, Sung Gap; Seo, Tae Seok

    2016-04-15

    A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (μPCR) and micro-capillary electrophoresis (μCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1 μL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, μPCR, and μCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-μPCR-μCE microdevice by using 1 μL whole human blood within 60 min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer. PMID:26657593

  10. New species of Ehrlichia isolated from Rhipicephalus (Boophilus) microplus shows an ortholog of the E. canis major immunogenic glycoprotein gp36 with a new sequence of tandem repeats

    PubMed Central

    2012-01-01

    Background Ehrlichia species are the etiological agents of emerging and life-threatening tick-borne human zoonoses that inflict serious and fatal infections in companion animals and livestock. The aim of this paper was to phylogeneticaly characterise a new species of Ehrlichia isolated from Rhipicephalus (Boophilus) microplus from Minas Gerais, Brazil. Methods The agent was isolated from the hemolymph of Rhipicephalus (B.) microplus engorged females that had been collected from naturally infested cattle in a farm in the state of Minas Gerais, Brazil. This agent was then established and cultured in IDE8 tick cells. The molecular and phylogenetic analysis was based on 16S rRNA, groEL, dsb, gltA and gp36 genes. We used the maximum likelihood method to construct the phylogenetic trees. Results The phylogenetic trees based on 16S rRNA, groEL, dsb and gltA showed that the Ehrlichia spp isolated in this study falls in a clade separated from any previously reported Ehrlichia spp. The molecular analysis of the ortholog of gp36, the major immunoreactive glycoproteins in E. canis and ortholog of the E. chaffeensis gp47, showed a unique tandem repeat of 9 amino acids (VPAASGDAQ) when compared with those reported for E. canis, E. chaffeensis and the related mucin-like protein in E. ruminantium. Conclusions Based on the molecular and phylogenetic analysis of the 16S rRNA, groEL, dsb and gltA genes we concluded that this tick-derived microorganism isolated in Brazil is a new species, named E. mineirensis (UFMG-EV), with predicted novel antigenic properties in the gp36 ortholog glycoprotein. Further studies on this new Ehrlichia spp should address questions about its transmissibility by ticks and its pathogenicity for mammalian hosts. PMID:23231731

  11. Genotyping of Brucella melitensis strains from dromedary camels (Camelus dromedarius) from the United Arab Emirates with multiple-locus variable-number tandem repeat analysis.

    PubMed

    Gyuranecz, Miklós; Wernery, Ulli; Kreizinger, Zsuzsa; Juhász, Judit; Felde, Orsolya; Nagy, Péter

    2016-04-15

    Camel brucellosis is a widespread zoonotic disease in camel-rearing countries caused by Brucella melitensis and Brucella abortus. The aim of this study was the first genetic analysis of B. melitensis strains isolated from dromedary camels (Camelus dromedarius) using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA 16 and its MLVA 8 and MLVA11 subsets were used to determine the genotypes of 15 B. melitensis isolates from dromedary camels (11 strains) and other host species (4 strains) from the United Arab Emirates and the results were then compared to B. melitensis MLVA genotypes from other parts of the world. Five, including two novel genotypes were identified with MLVA 8. MLVA 16 further discriminated these five genotypes to ten variants. The eleven camel isolates clustered into four main genetic groups within the East-Mediterranean and African clades and this clustering correlated with the geographic origin of the hosts (United Arab Emirates, Kingdom of Saudi Arabia and Sudan) and the date of their isolation. The camel strains were also genetically related to strains isolated from wild and domestic ruminants from their close habitat or from other parts of the world. Although limited number of strains were analysed, based on our data imported animals from foreign countries, local small ruminants and wildlife species are hypothesized to be the main sources of camel brucellosis in the United Arab Emirates. MLVA was successfully applied to determine the epidemiological links between the different camel B. melitensis infections in the United Arab Emirates and it can be a beneficial tool in future disease control programs. PMID:27016751

  12. Multilocus variable-number of tandem-repeats analysis of Salmonella enterica serotype Gallinarum and comparison with pulsed-field gel electrophoresis genotyping.

    PubMed

    Bergamini, Federica; Iori, Alessandra; Massi, Paola; Pongolini, Stefano

    2011-05-01

    Salmonella enterica serovar Gallinarum is the causative agent of fowl typhoid, a severe disease of poultry, responsible for heavy economic losses. Epidemiologic investigation of fowl typhoid significantly benefits from molecular typing tools, RAPD and PFGE have been proposed for this purpose. PFGE, a well established technique, is still the gold standard among typing methods for most bacteria, including salmonella. Nevertheless, it has some limitations regarding execution and reproducibility, in particular it is labour intensive and requires good technical expertise. Furthermore, it needs accurate standardization and results can be ambiguous to interpret. Such limitations can hamper reproducibility and transfer of results. As a possible alternative to PFGE, multilocus variable-number of tandem-repeats analysis (MLVA) has recently emerged as an effective genotyping method for many bacterial pathogens showing high discriminatory power associated to robustness. We developed a six-loci MLVA protocol for Salmonella Gallinarum and compared it to PFGE performed with SpeI, XbaI and NotI on fifty isolates. The proposed MLVA has a high discriminatory power, equivalent to that of the three-enzyme PFGE (Simpson's index 0.94 for MLVA, 0.93 for three-enzyme PFGE) but it is simpler to perform and straightforward in genotype identification, allowing unambiguous exchange of results. Stability of selected VNTR loci, assessed in vitro and in vivo, is good but not absolute, reflecting the sensitivity of MLVA to detect evolutionary changes of bacteria. Clustering of the isolates as determined by MLVA typing is substantially confirmed by PFGE. PMID:21208755

  13. Self-assembly of a peptide with a tandem repeat of the Aβ16-22 sequence linked by a β turn-promoting dipeptide sequence.

    PubMed

    Sivakama Sundari, Chandrasekaran; Bikshapathy, Erugurala; Nagaraj, Ramakrishnan

    2015-11-01

    Amyloid deposits have been found to be abundant in patients with Alzheimer's disease due to fibril formation by the Aβ peptides. Peptide Aβ16-22, comprising of the seven-residue segment KLVFFAE, spanning residues 16-22 of the full length Aβ42 peptide, aggregates to form fibrils or other nanostructures in isolation, depending on the conditions of dissolution and incubation. In this study, we have examined the self-assembly of PAβ, a tandem repeat peptide of the Aβ16-22 sequence, joined by a β-turn-inducing sequence Asn-Gly. To study the effect of various solvents on the self-association, hexafluoroisopropanol (HFIP), trifluoroethanol (TFE) and methanol were used. The peptide was also incubated in fibril-promoting conditions of 20% fluorinated alcohol-water mixtures which form dynamical solvent clusters, as well as in 20% MeOH-water mixture which does not form solvent clusters. Secondary structural studies suggest the presence of β-structures. Electron microscopic images indicate that fibril formation occurs in a time-dependent manner, under different conditions of solvent composition. Thioflavin-T fluorescence studies confirm the presence of amyloid fibrils in the aggregates. Although the insertion of the Asn-Gly sequence has not facilitated the formation of an ideal Type I' rigid turn, the intramolecular interactions aid the formation of a flexible β-turn conformation, with twisted β-sheets. Interactions between the intermolecular β-sheets result in the formation of amyloid fibrils. Organic solvents appear to play an important role in modulating self-assembly of peptide PAβ during fibril formation. Studies on β-hairpin engineered amyloidogenic peptides could lead to knowledge about suitable conditions for generating a diverse range of polymorphic structures. PMID:26473431

  14. Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

    SciTech Connect

    Liao, D.; Weiner, A.M.

    1995-12-10

    The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to study the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.

  15. Short tandem repeat (STR) genotyping of keratinised hair. Part 2. An optimised genomic DNA extraction procedure reveals donor dependence of STR profiles.

    PubMed

    McNevin, Dennis; Wilson-Wilde, Linzi; Robertson, James; Kyd, Jennelle; Lennard, Chris

    2005-10-29

    A feasibility study of short tandem repeat (STR) genotyping of telogen phase hairs in particular, and hair shaft in general, is presented. A number of extraction procedures in common use were investigated and the quantities of nuclear DNA (nuDNA) delivered were quantified via a real-time PCR assay. The extracts were subjected to two variations on AmpFlSTR Profiler Plus PCR amplification strategies (extended cycles, two rounds of PCR) and the genotypes compared. Nuclear DNA was found to persist in human hair shafts, albeit at very low levels. Full Profiler Plus profiles consistent with the hair donor were obtained from 100 mg hair shaft samples (bleached and unbleached). These were, however, mixed profiles, indicating low copy number (LCN) contamination in the extracts. Single telogen hair clubs and single hair shafts delivered partial profiles with usually only one allele of heterozygous loci. Telogen phase hairs yielded the same amount of nuDNA (and no more) as hair shafts (either anagen or telogen). Whether hair shafts dissolved or not in lysis buffer had no effect on either the quantitated yield of DNA or on the chance of obtaining a correct genotype. These results provide evidence that genomic DNA resides on the exterior of the hair shaft and we use this information to suggest an optimal procedure for nuDNA extraction from keratinised hair samples: soaking hairs in simple digestion buffers containing Tris-HCl, a salt and a chelating agent without prior cleaning of the hair shafts. It is proposed that cleaning removes most of the recoverable DNA. This procedure was applied to obtain genotypes from 3 cm hair shafts which matched reference profiles from the donors at up to 9 out of 10 AmpFlSTR Profiler Plus STR loci. When the genotyping success was measured by counting the number of matches between the two dominant alleles at each locus for each extract with the reference DNA profile of the hair donor, the success was found to be highly dependent on the donor. The

  16. Cytochrome P450 2E1 variable number tandem repeat polymorphisms and health risks: a genotype-phenotype study in cancers associated with drinking and/or smoking.

    PubMed

    Catanzaro, Irene; Naselli, Flores; Saverini, Marghereth; Giacalone, Antonio; Montalto, Giuseppe; Caradonna, Fabio

    2012-08-01

    Cytochrome P450 2E1 (CYP2E1) is one of the main enzymes involved in the oxidation of ethanol and in the transformation of a number of potentially dangerous compounds. It has various polymorphic sites, one of which is a variable number tandem repeat (VNTR) polymorphism previously described in the 5'-flanking region. The aim of this study was to investigate the genotype-phenotype association between CYP2E1 VNTR polymorphisms and risky health habits in healthy subjects and to analyze the associations between these polymorphisms with drinking- and/or smoking-related cancers. We analyzed 166 healthy subjects by genotyping for the CYP2E1 VNTR polymorphism associated with drinking and/or smoking habits by the more sensitive restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) method, using the NlaIV restriction enzyme. Sixty cases of pancreatic adenocarcinoma (PA) and 66 with hepatocellular carcinoma (HCC), were also genotyped. Statistical analysis was carried out to investigate the genotype-phenotype associations and to compare certain genotypes and cancer. We found 7 genotypes both in the healthy subjects and patients. The A1/A1 genotype was observed to be mainly associated with non-drinkers and -smokers (87.5 and 75.0%, respectively); moreover it was never found in the PA or HCC patients. Conversely, a weak association between A2/A3 with smokers (45.8%) and A4/A4 with drinkers (53.9%) was detected. In addition, the A4/A4 genotype was found to be significantly associated to PA [odds ratio (OR)=3.25; 95% confidence interval (CI) 1.21-7.50]. Our data demonstrate that certain CYP2E1 VNTR genotypes are associated with drinking and/or smoking habits; consequently, they may contribute either to the decreased or increased risk of developing drinking- and/or smoking-related cancers. In particular, we hypothesize that the A1/A1 VNTR genotype may have a protective role against drinking- and/or smoking-related cancers, and that A4/A4 may be a high

  17. Identification of Skeletal Remains of Communist Armed Forces Victims During and After World War II: Combined Y-chromosome Short Tandem Repeat (STR) and MiniSTR Approach

    PubMed Central

    Marjanović, Damir; Durmić-Pašić, Adaleta; Kovačević, Lejla; Avdić, Jasna; Džehverović, Mirela; Haverić, Sanin; Ramić, Jasmin; Kalamujić, Belma; Bilela, Lada Lukić; Škaro, Vedrana; Projić, Petar; Bajrović, Kasim; Drobnič, Katja; Davoren, Jon; Primorac, Dragan

    2009-01-01

    Aim To report on the use of STR, Y-STRs, and miniSTRs typing methods in the identification of victims of revolutionary violence and crimes against humanity committed by the Communist Armed Forces during and after World War II in which bodies were exhumed from mass and individual graves in Slovenia. Methods Bone fragments and teeth were removed from human remains found in several small and closely located hidden mass graves in the Škofja Loka area (Lovrenska Grapa and Žolšče) and 2 individual graves in the Ljubljana area (Podlipoglav), Slovenia. DNA was isolated using the Qiagen DNA extraction procedure optimized for bone and teeth. Some DNA extracts required additional purification, such as N-buthanol treatment. The QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. Initially, PowerPlex 16 kit was used to simultaneously analyze 15 short tandem repeat (STR) loci. The PowerPlex S5 miniSTR kit and AmpFℓSTR® MiniFiler PCR Amplification Kit was used for additional analysis if preliminary analysis yielded weak partial or no profiles at all. In 2 cases, when the PowerPlex 16 profiles indicated possible relatedness of the remains with reference samples, but there were insufficient probabilities to call the match to possible male paternal relatives, we resorted to an additional analysis of Y-STR markers. PowerPlex® Y System was used to simultaneously amplify 12 Y-STR loci. Fragment analysis was performed on an ABI PRISM 310 genetic analyzer. Matching probabilities were estimated using the DNA-View software. Results Following the Y-STR analysis, 1 of the “weak matches” previously obtained based on autosomal loci, was confirmed while the other 1 was not. Combined standard STR and miniSTR approach applied to bone samples from 2 individual graves resulted in positive identifications. Finally, using the same approach on 11 bone samples from hidden mass grave Žološče, we were able to obtain 6 useful DNA profiles. Conclusion The results of

  18. Y-chromosome Short Tandem Repeat Intermediate Variant Alleles DYS392.2, DYS449.2, and DYS385.2 Delineate New Phylogenetic Substructure in Human Y-chromosome Haplogroup Tree

    PubMed Central

    Myres, Natalie M.; Ritchie, Kathleen H.; Lin, Alice A.; Hughes, Robert H.; Woodward, Scott R.; Underhill, Peter A.

    2009-01-01

    Aim To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. Methods Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles. Results We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently. Conclusions Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and Y-STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context. PMID:19480020

  19. Differences of Variable Number Tandem Repeats in XRCC5 Promoter Are Associated with Increased or Decreased Risk of Breast Cancer in BRCA Gene Mutation Carriers

    PubMed Central

    Cui, Jian; Luo, Jiangtao; Kim, Yeong C.; Snyder, Carrie; Becirovic, Dina; Downs, Bradley; Lynch, Henry; Wang, San Ming

    2016-01-01

    Ku80 is a subunit of the Ku heterodimer that binds to DNA double-strand break ends as part of the non-homologous end joining (NHEJ) pathway. Ku80 is also involved in homologous recombination (HR) via its interaction with BRCA1. Ku80 is encoded by the XRCC5 gene that contains a variable number tandem repeat (VNTR) insertion in its promoter region. Different VNTR genotypes can alter XRCC5 expression and affect Ku80 production, thereby affecting NHEJ and HR pathways. VNTR polymorphism is associated with multiple types of sporadic cancer. In this study, we investigated its potential association with familial breast cancer at the germline level. Using PCR, PAGE, Sanger sequencing, and statistical analyses, we compared VNTR genotypes in the XRCC5 promoter between healthy individuals and three types of familial breast cancer cases: mutated BRCA1 (BRCA1+), mutated BRCA2 (BRCA2+), and wild-type BRCA1/BRCA2 (BRCAx). We observed significant differences of VNTR genotypes between control and BRCA1+ group (P < 0.0001) and BRCA2+ group (P = 0.0042) but not BRCAx group (P = 0.2185), and the differences were significant between control and cancer-affected BRCA1+ cases (P < 0.0001) and BRCA2+ cases (P = 0.0092) but not cancer-affected BRCAx cases (P = 0.4251). Further analysis indicated that 2R/2R (OR = 1.94, 95%CI = 1.26–2.95, P = 0.0096) and 2R/1R (OR = 1.58, 95%CI = 1.11–2.26, P = 0.0388) were associated with increased risk but 1R/1R (OR = 0.55, 95%CI = 0.35–0.84, P = 0.0196) and 1R/0R (OR = 0, 95%CI = 0–0.29, P = 0.0012) were associated with decreased risk in cancer-affected BRCA1+ group; 2R/1R (OR = 1.94, 95%CI = 1.14–3.32, P = 0.0242) was associated with increased risk in cancer-affected BRCA2+ group. No correlation was observed for the altered risk between cancer-affected or -unaffected carriers and between different age of cancer diagnosis in cancer-affected carriers. The frequently

  20. The structure of the ankyrin-binding site of [beta]-spectrin reveals how tandem spectrin-repeats generate unique ligand-binding properties

    SciTech Connect

    Stabach, Paul R.; Simonovic, Ivana; Ranieri, Miranda A.; Aboodi, Michael S.; Steitz, Thomas A.; Simonovic, Miljan; Morrow, Jon S.

    2009-09-02

    Spectrin and ankyrin participate in membrane organization, stability, signal transduction, and protein targeting; their interaction is critical for erythrocyte stability. Repeats 14 and 15 of {beta}I-spectrin are crucial for ankyrin recognition, yet the way spectrin binds ankyrin while preserving its repeat structure is unknown. We have solved the crystal structure of the {beta}I-spectrin 14,15 di-repeat unit to 2.1 {angstrom} resolution and found 14 residues critical for ankyrin binding that map to the end of the helix C of repeat 14, the linker region, and the B-C loop of repeat 15. The tilt (64{sup o}) across the 14,15 linker is greater than in any published di-repeat structure, suggesting that the relative positioning of the two repeats is important for ankyrin binding. We propose that a lack of structural constraints on linker and inter-helix loops allows proteins containing spectrin-like di-repeats to evolve diverse but specific ligand-recognition sites without compromising the structure of the repeat unit. The linker regions between repeats are thus critical determinants of both spectrin's flexibility and polyfunctionality. The putative coupling of flexibility and ligand binding suggests a mechanism by which spectrin might participate in mechanosensory regulation.

  1. Y-chromosome Short Tandem Repeat DYS458.2 Non-consensus Alleles Occur Independently in Both Binary Haplogroups J1-M267 and R1b3-M405

    PubMed Central

    Myres, Natalie M.; Ekins, Jayne E.; Lin, Alice A.; Cavalli-Sforza, L. Luca; Woodward, Scott R.; Underhill, Peter A.

    2007-01-01

    Aim To determine the human Y-chromosome haplogroup backgrounds of non-consensus DYS458.2 short tandem repeat alleles and evaluate their phylogenetic substructure and frequency in representative samples from the Middle East, Europe, and Pakistan. Methods Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci, including DYS388 to construct haplotypes. DNA sequencing of the DYS458 locus and median-joining network analyses were used to evaluate Y-chromosome lineages displaying the DYS458.2 motif. Results We showed that the DYS458.2 allelic innovation arose independently on at least two distinctive binary haplogroup backgrounds and possibly a third as well. The partial allele length pattern was fixed in all haplogroup J1 chromosomes examined, including its known rare sub-haplogroups. Within the alternative R1b3 associated M405 defined sub-haplogroup, both DYS458.0 and DYS458.2 allele classes occurred. A single chromosome also allocated to the R1b3-M269*(xM405) classification. The physical position of the partial insertion/deletion occurrence within the normal tetramer tract differed distinctly in each haplogroup context. Conclusions While unusual DYS458.2 alleles are informative, additional information for other linked polymorphic loci is required when using such non-conforming alleles to infer haplogroup background and common ancestry. PMID:17696299

  2. New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

    PubMed Central

    Poulin, L.; Grygiel, P.; Magne, M.; Rodriguez-R, L. M.; Forero Serna, N.; Zhao, S.; El Rafii, M.; Dao, S.; Tekete, C.; Wonni, I.; Koita, O.; Pruvost, O.; Verdier, V.; Vernière, C.

    2014-01-01

    Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales. PMID:25398857

  3. Tandem betatron

    DOEpatents

    Keinigs, Rhonald K.

    1992-01-01

    Two betatrons are provided in tandem for alternately accelerating an electron beam to avoid the single flux swing limitation of conventional betatrons and to accelerate the electron beam to high energies. The electron beam is accelerated in a first betatron during a period of increasing magnetic flux. The eletron beam is extracted from the first betatron as a peak magnetic flux is reached and then injected into a second betatron at a time of minimum magnetic flux in the second betatron. The cycle may be repeated until the desired electron beam energy is obtained. In one embodiment, the second betatron is axially offset from the first betatron to provide for electron beam injection directly at the axial location of the beam orbit in the second betatron.

  4. A highly polymorphic (ACT)n VNTR (variable nucleotide of tandem repeats) locus inside intron 12 of COL1A2, one of the two genes involved in dominant osteogenesis imperfecta.

    PubMed

    Pepe, G

    1993-01-01

    A new, highly polymorphic, region consisting of variable number of tandem repeats (VNTR) is described that occurs within intron 12 of the COL1A2 gene. This VNTR consists of the trinucleotide ACT repeated from 6 to 12 times. Of the six alleles so far detected four are common in the three major races. The two rare alleles, (ACT)11 and (ACT)12, have been found only in Africans. In addition, a rapid technique has been developed that can be used successfully with very small amounts of even partially degraded DNA, thus allowing the use of this VNTR for forensic applications. Since dominant OI can be due to mutations at either of two loci (COL1A1 and COL1A2) prenatal diagnosis becomes feasible in the majority of the affected families only if a very informative marker is available for both of these genes. This VNTR provides a very powerful marker for COL1A2. In fact the heterozygosity for it ranges from 0.634 to 0.741 with PIC values from 0.562 to 0.696, respectively. Since trinucleotide repeats can be "unstable," and sometimes pathogenic, the unexplained collagenopathies (or suspected collagenopathies) should be analyzed from this point of view. PMID:8104634

  5. Tandem repeats of the extracellular domain of Matrix 2 influenza protein exposed in Brucella lumazine synthase decameric carrier molecule induce protection in mice.

    PubMed

    Alvarez, Paula; Zylberman, Vanesa; Ghersi, Giselle; Boado, Lorena; Palacios, Carlos; Goldbaum, Fernando; Mattion, Nora

    2013-01-21

    The antigenic variation of influenza virus represents a major prevention problem. However, the ectodomain of the protein Matrix 2 (M2e) is nearly invariant in all human influenza A strains and has been considered as a promising candidate for a broadly protective vaccine because antibodies to M2e are protective in animal models. In this work we evaluated the possible use of Brucella abortus lumazine synthase protein (BLS), a highly immunogenic decameric protein, as a carrier of the M2e peptide. Chimeric proteins generated by the fusion of one or four in tandem copies of M2e to BLS were efficiently expressed in Escherichia coli and assembled in decameric subunits similarly to the wild type BLS enzyme, as demonstrated by the comparative circular dichroism spectra and size exclusion chromatography and static light scattering analysis. The M2e peptides were stably exposed at the ten N-terminal ends of each BLS molecule. Immunization of mice with purified chimeras carrying only one M2e (BLS-M2e) copy elicited a significant humoral immune response with the addition of different adjuvants. The fusion of four in tandem copies of the M2e peptide (BLS-4M2e) resulted in similar levels of humoral immune response but in the absence of adjuvant. Survival of mice challenged with live influenza virus was 100% after vaccination with BLS-4M2e adjuvanted with Iscomatrix(®) (P<0.001) and 80% when adjuvanted with alum (P<0.01), while the chimera alone protected 60% of the animals (P<0.05). The approach described in this study is intended as a contribution to the generation of universal influenza immunogens, through a simple production and purification process and using safe carriers that might eventually avoid the use of strong adjuvants. PMID:23246552

  6. A Further Analysis of the Relationship between Yellow Ripe-Fruit Color and the Capsanthin-Capsorubin Synthase Gene in Pepper (Capsicum sp.) Indicated a New Mutant Variant in C. annuum and a Tandem Repeat Structure in Promoter Region

    PubMed Central

    Gui, Xiao-Ling; Chang, Xiao-Bei; Gong, Zhen-Hui

    2013-01-01

    Mature pepper (Capsicum sp.) fruits come in a variety of colors, including red, orange, yellow, brown, and white. To better understand the genetic and regulatory relationships between the yellow fruit phenotype and the capsanthin-capsorubin synthase gene (Ccs), we examined 156 Capsicum varieties, most of which were collected from Northwest Chinese landraces. A new ccs variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the C. annuum species, has low genetic similarity to other yellow C. annuum varieties. In the coding sequence of this ccs allele, we detected a premature stop codon derived from a C to G change, as well as a downstream frame-shift caused by a 1-bp nucleotide deletion. In addition, the expression of the gene was detected in mature CK7 fruit. Furthermore, the promoter sequences of Ccs from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all C. annuum varieties examined in this study, the repeat number was three, compared with four in two C. chinense accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative cis-elements were also found in every repeat. This suggests that the transcriptional regulation of Ccs expression is complex. Based on the analysis of the novel C. annuum mutation reported here, along with the studies of three mutation types in yellow C. annuum and C. chinense accessions, we suggest that the mechanism leading to the production of yellow color fruit may be not as complex as that leading to orange fruit production. PMID:23637942

  7. An immunogen containing four tandem 10E8 epitope repeats with exposed key residues induces antibodies that neutralize HIV-1 and activates an ADCC reporter gene.

    PubMed

    Sun, Zhiwu; Zhu, Yun; Wang, Qian; Ye, Ling; Dai, Yanyan; Su, Shan; Yu, Fei; Ying, Tianlei; Yang, Chinglai; Jiang, Shibo; Lu, Lu

    2016-01-01

    After three decades of intensive research efforts, an effective vaccine against HIV-1 remains to be developed. Several broadly neutralizing antibodies to HIV-1, such as 10E8, recognize the membrane proximal external region (MPER) of the HIV-1 gp41 protein. Thus, the MPER is considered to be a very important target for vaccine design. However, the MPER segment has very weak immunogenicity and tends to insert its epitope residues into the cell membrane, thereby avoiding antibody binding. To address this complication in vaccine development, we herein designed a peptide, designated 10E8-4P, containing four copies of the 10E8 epitope as an immunogen. As predicted by structural simulation, 10E8-4P exhibits a well-arranged tandem helical conformation, with the key residues in the 10E8 epitope oriented at different angles, thus suggesting that some of these key residues may be exposed outside of the lipid membrane. Compared with a peptide containing a single 10E8 epitope (10E8-1P), 10E8-4P not only exhibited better antigenicity but also elicited neutralizing antibody response against HIV-1 pseudoviruses, whereas 10E8-1P could not induce detectable neutralizing antibody response. Importantly, antibodies elicited by 10E8-4P also possessed a strong ability to activate an antibody-dependent cell-mediated cytotoxicity (ADCC) reporter gene, thus suggesting that they may have ADCC activity. Therefore, this strategy shows promise for further optimization and application in future HIV-1 vaccine design. PMID:27329850

  8. An immunogen containing four tandem 10E8 epitope repeats with exposed key residues induces antibodies that neutralize HIV-1 and activates an ADCC reporter gene

    PubMed Central

    Sun, Zhiwu; Zhu, Yun; Wang, Qian; Ye, Ling; Dai, Yanyan; Su, Shan; Yu, Fei; Ying, Tianlei; Yang, Chinglai; Jiang, Shibo; Lu, Lu

    2016-01-01

    After three decades of intensive research efforts, an effective vaccine against HIV-1 remains to be developed. Several broadly neutralizing antibodies to HIV-1, such as 10E8, recognize the membrane proximal external region (MPER) of the HIV-1 gp41 protein. Thus, the MPER is considered to be a very important target for vaccine design. However, the MPER segment has very weak immunogenicity and tends to insert its epitope residues into the cell membrane, thereby avoiding antibody binding. To address this complication in vaccine development, we herein designed a peptide, designated 10E8-4P, containing four copies of the 10E8 epitope as an immunogen. As predicted by structural simulation, 10E8-4P exhibits a well-arranged tandem helical conformation, with the key residues in the 10E8 epitope oriented at different angles, thus suggesting that some of these key residues may be exposed outside of the lipid membrane. Compared with a peptide containing a single 10E8 epitope (10E8-1P), 10E8-4P not only exhibited better antigenicity but also elicited neutralizing antibody response against HIV-1 pseudoviruses, whereas 10E8-1P could not induce detectable neutralizing antibody response. Importantly, antibodies elicited by 10E8-4P also possessed a strong ability to activate an antibody-dependent cell-mediated cytotoxicity (ADCC) reporter gene, thus suggesting that they may have ADCC activity. Therefore, this strategy shows promise for further optimization and application in future HIV-1 vaccine design. PMID:27329850

  9. Calcium binding to tandem repeats of EGF-like modules. Expression and characterization of the EGF-like modules of human Notch-1 implicated in receptor-ligand interactions.

    PubMed Central

    Rand, M. D.; Lindblom, A.; Carlson, J.; Villoutreix, B. O.; Stenflo, J.

    1997-01-01

    The Ca(2+)-binding epidermal growth factor (cbEGF)-like module is a structural component of numerous diverse proteins and occurs almost exclusively within repeated motifs. Notch-1, a fundamental receptor for cell fate decisions, contains 36 extracellular EGF modules in tandem, of which 21 are potentially Ca(2+)-binding. We report the Ca(2+)-binding properties of EGF11-12 and EGF10-13 from human Notch-1 (hNEGF11-12 and hNEGF10-13), modules previously shown to support Ca(2+)-dependent interactions with the ligands Delta and Serrate. Ca2+ titrations in the presence of chromophoric chelators, 5,5'-Br2BAPTA and 5-NBAPTA, gave two binding constants for hNEGF11-12, Kd1 = 3.4 x 10(-5) M and Kd2 > 2.5 x 10(-4) M. The high-affinity site was found to be localized to hNEGF12. Titration of hNEGF10-13 gave three binding constants, Kd1 = 3.1 x 10(-6) M, Kd2 = 1.6 x 10(-4) M, and Kd3 > 2.5 x 10(-4) M, demonstrating that assembly of EGF modules in tandem can increase Ca2+ affinity. The highest affinity sites in hNEGF11-12 and hNEGF10-13 had 10 to 100-fold higher affinity than reported for EGF32-33 and EGF25-31, respectively, from fibrillin-1, a connective tissue protein with 43 cbEGF modules. A model of hNEGF11-12 based on fibrillin-1 EGF32-33 demonstrates electronegative potential that could contribute to the higher affinity of the Ca(2+)-binding site in hNEGF12. These data demonstrate that the Ca2+ affinity of cbEGF repeats can be highly variable among different classes of cbEGF containing proteins. PMID:9336830

  10. Sequence alignment with tandem duplication

    SciTech Connect

    Benson, G.

    1997-12-01

    Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.

  11. Unravelling evolution of Nanog, the key transcription factor involved in self-renewal of undifferentiated embryonic stem cells, by pattern recognition in nucleotide and tandem repeats characteristics.

    PubMed

    Pashaiasl, Maryam; Khodadadi, Khodadad; Kayvanjoo, Amir Hossein; Pashaei-Asl, Roghiyeh; Ebrahimie, Esmaeil; Ebrahimi, Mansour

    2016-03-10

    Nanog, an important transcription factor in embryonic stem cells (ESC), is the key factor in maintaining pluripotency to establish ESC identity and has the ability to induce embryonic germ layers. Nanog is responsible for self-renewal and pluripotency of stem cells as well as cancer invasiveness, tumor cell proliferation, motility and drug-resistance. Understanding the underlying mechanisms of Nanog evolution and regulation can lead to future advances in treatment of cancers. Recent integration of machine learning models with genetics has provided a powerful tool for knowledge discovery and uncovering evolutionary pathways. Herein, sequences of 47 Nanog genes from various species were extracted and two datasets of features were computationally extracted from these sequences. At the first dataset, 76 nucleotide acid attributes were calculated for each Nanog sequence. The second dataset was prepared based on the 10,480 repeated nucleotide sequences (from 5 to 50bp lengths). Then, various data mining algorithms such as decision tree models were applied on these datasets to find the evolutionary pathways of Nanog diversion. Attribute weighting models were highlighted features such as the frequencies of AA and GC as the most important genomic features in Nanog gene classification and differentiation. Similar findings were obtained by tree induction algorithms. Results from the second database showed that some short sequence strings, such as ACTACT, TCCTGA, CCTGA, GAAGAC, and TATCCC can be effectively used to identify Nanog genes in various species. The outcomes of this study, for the first time, unravels the importance of particular genomic features in Nanog gene evolution paving roads toward better understanding of stem cell development and human targeted disorder therapy. PMID:26687709

  12. Optimized Multilocus Variable-Number Tandem-Repeat Analysis Assay and Its Complementarity with Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing for Listeria monocytogenes Clone Identification and Surveillance

    PubMed Central

    Chenal-Francisque, Viviane; Diancourt, Laure; Cantinelli, Thomas; Passet, Virginie; Tran-Hykes, Coralie; Bracq-Dieye, Hélène; Leclercq, Alexandre; Pourcel, Christine

    2013-01-01

    Populations of the food-borne pathogen Listeria monocytogenes are genetically structured into a small number of major clonal groups, some of which have been implicated in multiple outbreaks. The goal of this study was to develop and evaluate an optimized multilocus variable number of tandem repeat (VNTR) analysis (MLVA) subtyping scheme for strain discrimination and clonal group identification. We evaluated 18 VNTR loci and combined the 11 best ones into two multiplexed PCR assays (MLVA-11). A collection of 255 isolates representing the diversity of clonal groups within phylogenetic lineages I and II, including representatives of epidemic clones, were analyzed by MLVA-11, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). MLVA-11 had less discriminatory power than PFGE, except for some clones, and was unable to distinguish some epidemiologically unrelated isolates. Yet it distinguished all major MLST clones and therefore constitutes a rapid method to identify epidemiologically relevant clonal groups. Given its high reproducibility and high throughput, MLVA represents a very attractive first-line screening method to alleviate the PFGE workload in outbreak investigations and listeriosis surveillance. PMID:23576539

  13. Precision and accuracy in fluorescent short tandem repeat DNA typing: assessment of benefits imparted by the use of allelic ladders with the AmpF/STR Profiler Plus kit.

    PubMed

    Leclair, Benoît; Frégeau, Chantal J; Bowen, Kathy L; Fourney, Ron M

    2004-03-01

    Base-calling precision of short tandem repeat (STR) allelic bands on dynamic slab-gel electrophoresis systems was evaluated. Data was collected from over 6000 population database allele peaks generated from 468 population database samples amplified with the AmpF/STR Profiler Plus (PP) kit and electrophoresed on ABD 377 DNA sequencers. Precision was measured by way of standard deviations and was shown to be essentially the same, whether using fixed or floating bin genotyping. However, the allelic ladders have proven more sensitive to electrophoretic variations than database samples, which have caused some floating bins of D18S51 to shift on occasion. This observation prompted the investigation of polyacrylamide gel formulations in order to stabilize allelic ladder migration. The results demonstrate that, although alleles comprised in allelic ladders and questioned samples run on the same gel should migrate in an identical manner, this premise needs to be verified for any given electrophoresis platform and gel formulation. We show that the compilation of base-calling data is a very informative and useful tool for assessing the performance stability of dynamic gel electrophoresis systems, stability on which depends genotyping result quality. PMID:15004837

  14. AmpFlSTR profiler Plus short tandem repeat DNA analysis of casework samples, mixture samples, and nonhuman DNA samples amplified under reduced PCR volume conditions (25 microL).

    PubMed

    Frégeau, Chantal J; Bowen, Kathy L; Leclair, Benoît; Trudel, Isabelle; Bishop, Lucy; Fourney, Ron M

    2003-09-01

    As part of the validation of the AmpFlSTR Profiler Plus short tandem repeat (STR) system, under reduced polymerase chain reaction (PCR) volume conditions (i.e., 25 microL), a total of 275 casework samples were processed. Examples of profiles are presented along with amplification conditions to improve the odds of obtaining balanced and complete profiles for samples showing partial results or profiles with a descending slope. Data collected and used to develop our interpretation guidelines are included. From the mixture studies, full profiles were obtained for minor contributors, using 2 ng of DNA, with ratios of 10:1 or 1:20 and using 1 ng of DNA, with ratios of 10:1 and 1:8. The specificity of the Profiler Plus amplification reaction performed in 25 microL was examined and confirmed using a large spectrum of nonhuman DNAs. This report supports the use of the AmpFlSTR Profiler Plus STR system for casework DNA typing under reduced PCR volume conditions. PMID:14535664

  15. Pseudomonas aeruginosa Outbreak Linked to Mineral Water Bottles in a Neonatal Intensive Care Unit: Fast Typing by Use of High-Resolution Melting Analysis of a Variable-Number Tandem-Repeat Locus▿ †

    PubMed Central

    Naze, F.; Jouen, E.; Randriamahazo, R. T.; Simac, C.; Laurent, P.; Blériot, A.; Chiroleu, F.; Gagnevin, L.; Pruvost, O.; Michault, A.

    2010-01-01

    Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial infections in intensive care units. Determining a system of typing that is discriminatory is essential for epidemiological surveillance of P. aeruginosa. We developed a method for the typing of Pseudomonas aeruginosa, namely, multiple-locus variable-number tandem-repeat (VNTR) typing with high-resolution melting analysis (HRMA). The technology was used to genotype a collection of 43 environmental and clinical strains isolated during an outbreak in a neonatal intensive care unit (NICU) that we report. Nineteen strains isolated in other departments or outside the hospital were also tested. The genetic diversity of this collection was determined using VNTR-HRMA, with amplified fragment length polymorphism (AFLP) analysis as a reference. Twenty-five and 28 genotypes were identified, respectively, and both techniques produced congruent data. VNTR-HRMA established clonal relationships between the strains of P. aeruginosa isolated during the outbreak in the NICU and proved, for the first time, the role of mineral water as the inoculum source. VNTR typing with one primer pair in association with HRMA is highly reproducible and discriminative, easily portable among laboratories, fast, and inexpensive, and it demonstrated excellent typeability in this study. VNTR-HRMA represents a promising tool for the molecular surveillance of P. aeruginosa and perhaps for molecular epidemiologic analysis of other hospital infections. PMID:20573865

  16. Phosphate Control of Oxytetracycline Production by Streptomyces rimosus Is at the Level of Transcription from Promoters Overlapped by Tandem Repeats Similar to Those of the DNA-Binding Sites of the OmpR Family

    PubMed Central

    McDowall, Kenneth J.; Thamchaipenet, Arinthip; Hunter, Iain S.

    1999-01-01

    Physiological studies have shown that Streptomyces rimosus produces the polyketide antibiotic oxytetracycline abundantly when its mycelial growth is limited by phosphate starvation. We show here that transcripts originating from the promoter for one of the biosynthetic genes, otcC (encoding anhydrotetracycline oxygenase), and from a promoter for the divergent otcX genes peak in abundance at the onset of antibiotic production induced by phosphate starvation, indicating that the synthesis of oxytetracycline is controlled, at least in part, at the level of transcription. Furthermore, analysis of the sequences of the promoters for otcC, otcX, and the polyketide synthase (otcY) genes revealed tandem repeats having significant similarity to the DNA-binding sites of ActII-Orf4 and DnrI, which are Streptomyces antibiotic regulatory proteins (SARPs) related to the OmpR family of transcription activators. Together, the above results suggest that oxytetracycline production by S. rimosus requires a SARP-like transcription factor that is either produced or activated or both under conditions of low phosphate concentrations. We also provide evidence consistent with the otrA resistance gene being cotranscribed with otcC as part of a polycistronic message, suggesting a simple mechanism of coordinate regulation which ensures that resistance to the antibiotic increases in proportion to production. PMID:10322002

  17. Emergence of a multidrug-resistant (ASSuTTm) strain of Salmonella enterica serovar Typhimurium DT120 in England in 2011 and the use of multiple-locus variable-number tandem-repeat analysis in supporting outbreak investigations.

    PubMed

    Paranthaman, Karthikeyan; Haroon, Sophie; Latif, Samia; Vinnyey, Natalie; de Souza, Valerie; Welfare, William; Tahir, Mamoona; Cooke, Edward; Stone, Kirsten; Lane, Chris; Peters, Tansy; Puleston, Richard

    2013-10-01

    In summer 2011, two outbreaks of a unique, multidrug-resistant strain of Salmonella enterica serovar Typhimurium phage type 120 (DT120) occurred mainly in the Midlands, England. The first outbreak occurred among guests attending a wedding in July 2011 ('Wedding outbreak'), followed by a more geographically dispersed outbreak in August and September 2011 ('Midlands outbreak'). Fifty-one cases were confirmed. Detailed epidemiological and environmental health investigations suggested that pork was the most likely source of both outbreaks. All human samples and one pork sample showed the specific multiple-locus variable-number tandem-repeat analysis (MLVA) profile 3-11-12-NA-0211, with at most two loci variations. Trace-back investigations suggested a link to a butcher's shop and a pig farm in the East Midlands. The investigations highlight the utility of molecular analysis (MLVA) in supporting epidemiological investigations of outbreaks caused by S. Typhimurium DT120. Safe handling and cooking of pork by food business operators and consumers are key interventions to prevent future outbreaks. PMID:23869962

  18. Ancestry of the Brazilian TP53 c.1010G>A (p.Arg337His, R337H) Founder Mutation: Clues from Haplotyping of Short Tandem Repeats on Chromosome 17p

    PubMed Central

    Paskulin, Diego Davila; Giacomazzi, Juliana; Achatz, Maria Isabel; Costa, Sandra; Reis, Rui Manoel; Hainaut, Pierre; dos Santos, Sidney Emanuel Batista; Ashton-Prolla, Patricia

    2015-01-01

    Rare germline mutations in TP53 (17p13.1) cause a highly penetrant predisposition to a specific spectrum of early cancers, defining the Li-Fraumeni Syndrome (LFS). A germline mutation at codon 337 (p.Arg337His, c1010G>A) is found in about 0.3% of the population of Southern Brazil. This mutation is associated with partially penetrant LFS traits and is found in the germline of patients with early cancers of the LFS spectrum unselected for familial history. To characterize the extended haplotypes carrying the mutation, we have genotyped 9 short tandem repeats on chromosome 17p in 12 trios of Brazilian p.Arg337His carriers. Results confirm that all share a common ancestor haplotype of Caucasian/Portuguese-Iberic origin, distant in about 72–84 generations (2000 years assuming a 25 years intergenerational distance) and thus pre-dating European migration to Brazil. So far, the founder p.Arg337His haplotype has not been detected outside Brazil, with the exception of two residents of Portugal, one of them of Brazilian origin. On the other hand, increased meiotic recombination in p.Arg337His carriers may account for higher than expected haplotype diversity. Further studies comparing haplotypes in populations of Brazil and of other areas of Portuguese migration are needed to understand the historical context of this mutation in Brazil. PMID:26618902

  19. Fuzzy Commitment

    NASA Astrophysics Data System (ADS)

    Juels, Ari

    The purpose of this chapter is to introduce fuzzy commitment, one of the earliest and simplest constructions geared toward cryptography over noisy data. The chapter also explores applications of fuzzy commitment to two problems in data security: (1) secure management of biometrics, with a focus on iriscodes, and (2) use of knowledge-based authentication (i.e., personal questions) for password recovery.

  20. Fuzzy logic

    NASA Technical Reports Server (NTRS)

    Zadeh, Lofti A.

    1988-01-01

    The author presents a condensed exposition of some basic ideas underlying fuzzy logic and describes some representative applications. The discussion covers basic principles; meaning representation and inference; basic rules of inference; and the linguistic variable and its application to fuzzy control.

  1. Tandem BRCT Domains

    PubMed Central

    Mesquita, Rafael D.; Woods, Nicholas T.; Seabra-Junior, Eloy S.; Monteiro, Alvaro N.A.

    2010-01-01

    The cell’s ability to sense and respond to specific stimuli is a complex system derived from precisely regulated protein-protein interactions. Some of these protein-protein interactions are mediated by the recognition of linear peptide motifs by protein modular domains. BRCT (BRCA1 C-terminal) domains and their linear motif counterparts, which contain phosphoserines, are one such pair-wise interaction system that seems to have evolved to serve as a surveillance system to monitor threats to the cell’s genetic integrity. Evidence indicates that BRCT domains found in tandem can cooperate to provide sequence-specific binding of phosphorylated peptides as is the case for the breast and ovarian cancer susceptibility gene BRCA1 and the PAX transcription factor–interacting protein PAXIP1. Particular interest has been paid to tandem BRCT domains as “readers” of signaling events in the form of phosphorylated serine moieties induced by the activation of DNA damage response kinases ATM, ATR, and DNA-PK. However, given the diversity of tandem BRCT-containing proteins, questions remain as to the origin and evolution of this domain. Here, we discuss emerging views of the origin and evolving roles of tandem BRCT domain repeats in the DNA damage response. PMID:21533002

  2. Use of multiple-locus variable-number tandem repeat analysis to evaluate Escherichia coli O157 subtype distribution and transmission dynamics following natural exposure on a closed beef feedlot facility.

    PubMed

    Williams, Michele L; Pearl, David L; Bishop, Katherine E; Lejeune, Jeffrey T

    2013-10-01

    To better understand the epizootiology of Escherichia coli O157:H7 among cattle, all E. coli O157 isolates recovered on a research feedlot during a single feeding period were characterized by multiple-locus variable-number tandem repeat analysis (MLVA). Three distinct MLVA subtypes (A, B, C), accounting for 24%, 15%, and 64% of total isolates, respectively, were identified. Subtypes A and B were isolated at the initiation of sampling, but their prevalence waned and subtype C, first isolated on the third sampling date, became the predominant subtype on the feedlot. Supershedding events, however, occurred with equal frequency for all three MLVA-types. Using a multilevel logistic regression model, we investigated whether the odds of shedding subtype C relative to subtypes A or B were associated with time, diet, or the presence of a penmate shedding high numbers of subtype C. Only time and exposure to an animal shedding MLVA-type C at 10³ colony-forming units or greater in the pen at the time of sampling were significantly associated with increased shedding of subtype C. High-level shedding of those E. coli O157 subtypes better suited for survival in the environment and/or in the host appear to play a significant role in the development of predominant E. coli O157 subtypes. Supershedding events alone are neither required nor sufficient to drive the epidemiology of specific E. coli O157 subtypes. Additional factors are necessary to direct successful on-farm transmission of E. coli O157. PMID:23859259

  3. Origin of the Outbreak in France of Pseudomonas syringae pv. actinidiae Biovar 3, the Causal Agent of Bacterial Canker of Kiwifruit, Revealed by a Multilocus Variable-Number Tandem-Repeat Analysis.

    PubMed

    Cunty, A; Cesbron, S; Poliakoff, F; Jacques, M-A; Manceau, C

    2015-10-01

    The first outbreaks of bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae biovar 3 were detected in France in 2010. P. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. P. syringae pv. actinidifoliorum, which is pathogenic on kiwi as well, causes only leaf spots. In order to conduct an epidemiological study to track the spread of the epidemics of these two pathogens in France, we developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA). MLVA was conducted on 340 strains of P. syringae pv. actinidiae biovar 3 isolated in Chile, China, France, Italy, and New Zealand and on 39 strains of P. syringae pv. actinidifoliorum isolated in Australia, France, and New Zealand. Eleven polymorphic VNTR loci were identified in the genomes of P. syringae pv. actinidiae biovar 3 ICMP 18744 and of P. syringae pv. actinidifoliorum ICMP 18807. MLVA enabled the structuring of P. syringae pv. actinidiae biovar 3 and P. syringae pv. actinidifoliorum strains in 55 and 16 haplotypes, respectively. MLVA and discriminant analysis of principal components revealed that strains isolated in Chile, China, and New Zealand are genetically distinct from P. syringae pv. actinidiae strains isolated in France and in Italy, which appear to be closely related at the genetic level. In contrast, no structuring was observed for P. syringae pv. actinidifoliorum. We developed an MLVA scheme to explore the diversity within P. syringae pv. actinidiae biovar 3 and to trace the dispersal routes of epidemic P. syringae pv. actinidiae biovar 3 in Europe. We suggest using this MLVA scheme to trace the dispersal routes of P. syringae pv. actinidiae at a global level. PMID:26209667

  4. Multilocus Variable-Number-Tandem-Repeats Analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium

    PubMed Central

    2013-01-01

    Background Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected in Belgium. The lack of a convenient high-resolution strain-typing method has hampered the study of the routes of transmission of Cmm and epidemiology in tomato cultivation. In this study the genetic relatedness among a worldwide collection of Cmm strains and their relatives was approached by gyrB and dnaA gene sequencing. Further, we developed and applied a multilocus variable number of tandem repeats analysis (MLVA) scheme to discriminate among Cmm strains. Results A phylogenetic analysis of gyrB and dnaA gene sequences of 56 Cmm strains demonstrated that Belgian Cmm strains from recent outbreaks of 2010–2012 form a genetically uniform group within the Cmm clade, and Cmm is phylogenetically distinct from other Clavibacter subspecies and from non-pathogenic Clavibacter-like strains. MLVA conducted with eight minisatellite loci detected 25 haplotypes within Cmm. All strains from Belgian outbreaks, isolated between 2010 and 2012, together with two French strains from 2010 seem to form one monomorphic group. Regardless of the isolation year, location or tomato cultivar, Belgian strains from recent outbreaks belonged to the same haplotype. On the contrary, strains from diverse geographical locations or isolated over longer periods of time formed mostly singletons. Conclusions We hypothesise that the introduction might have originated from one lot of seeds or contaminated tomato seedlings that was the source of the outbreak in 2010 and that these Cmm strains persisted and induced infection in 2011 and 2012. Our results demonstrate that MLVA is a promising typing technique for a local surveillance and outbreaks investigation in epidemiological studies of Cmm. PMID:23738754

  5. Origin of the Outbreak in France of Pseudomonas syringae pv. actinidiae Biovar 3, the Causal Agent of Bacterial Canker of Kiwifruit, Revealed by a Multilocus Variable-Number Tandem-Repeat Analysis

    PubMed Central

    Cunty, A.; Cesbron, S.; Poliakoff, F.; Jacques, M.-A.

    2015-01-01

    The first outbreaks of bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae biovar 3 were detected in France in 2010. P. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. P. syringae pv. actinidifoliorum, which is pathogenic on kiwi as well, causes only leaf spots. In order to conduct an epidemiological study to track the spread of the epidemics of these two pathogens in France, we developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA). MLVA was conducted on 340 strains of P. syringae pv. actinidiae biovar 3 isolated in Chile, China, France, Italy, and New Zealand and on 39 strains of P. syringae pv. actinidifoliorum isolated in Australia, France, and New Zealand. Eleven polymorphic VNTR loci were identified in the genomes of P. syringae pv. actinidiae biovar 3 ICMP 18744 and of P. syringae pv. actinidifoliorum ICMP 18807. MLVA enabled the structuring of P. syringae pv. actinidiae biovar 3 and P. syringae pv. actinidifoliorum strains in 55 and 16 haplotypes, respectively. MLVA and discriminant analysis of principal components revealed that strains isolated in Chile, China, and New Zealand are genetically distinct from P. syringae pv. actinidiae strains isolated in France and in Italy, which appear to be closely related at the genetic level. In contrast, no structuring was observed for P. syringae pv. actinidifoliorum. We developed an MLVA scheme to explore the diversity within P. syringae pv. actinidiae biovar 3 and to trace the dispersal routes of epidemic P. syringae pv. actinidiae biovar 3 in Europe. We suggest using this MLVA scheme to trace the dispersal routes of P. syringae pv. actinidiae at a global level. PMID:26209667

  6. Comparative Study of IS6110 Restriction Fragment Length Polymorphism and Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Isolates in the Netherlands, Based on a 5-Year Nationwide Survey

    PubMed Central

    de Beer, Jessica L.; van Ingen, Jakko; de Vries, Gerard; Erkens, Connie; Sebek, Maruschka; Mulder, Arnout; Sloot, Rosa; van den Brandt, Anne-Marie; Enaimi, Mimount; Kremer, Kristin; Supply, Philip

    2013-01-01

    In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a detailed evaluation on discriminatory power and agreement with findings in a cluster investigation was performed on 3,975 tuberculosis cases during the period of 2004 to 2008. The level of discrimination of the two typing methods did not differ substantially: RFLP typing yielded 2,733 distinct patterns compared to 2,607 in VNTR typing. The global concordance, defined as isolates labeled unique or identically distributed in clusters by both methods, amounted to 78.5% (n = 3,123). Of the remaining 855 cases, 12% (n = 479) of the cases were clustered only by VNTR, 7.7% (n = 305) only by RFLP typing, and 1.8% (n = 71) revealed different cluster compositions in the two approaches. A cluster investigation was performed for 87% (n = 1,462) of the cases clustered by RFLP. For the 740 cases with confirmed or presumed epidemiological links, 92% were concordant with VNTR typing. In contrast, only 64% of the 722 cases without an epidemiological link but clustered by RFLP typing were also clustered by VNTR typing. We conclude that VNTR typing has a discriminatory power equal to IS6110 RFLP typing but is in better agreement with findings in a cluster investigation performed on an RFLP-clustering-based cluster investigation. Both aspects make VNTR typing a suitable method for tuberculosis surveillance systems. PMID:23363841

  7. Housekeeping Gene Sequencing and Multilocus Variable-Number Tandem-Repeat Analysis To Identify Subpopulations within Pseudomonas syringae pv. maculicola and Pseudomonas syringae pv. tomato That Correlate with Host Specificity

    PubMed Central

    Gironde, S.

    2012-01-01

    Pseudomonas syringae pv. maculicola causes bacterial spot on Brassicaceae worldwide, and for the last 10 years severe outbreaks have been reported in the Loire Valley, France. P. syringae pv. maculicola resembles P. syringae pv. tomato in that it is also pathogenic for tomato and causes the same types of symptoms. We used a collection of 106 strains of P. syringae to characterize the relationships between P. syringae pv. maculicola and related pathovars, paying special attention to P. syringae pv. tomato. Phylogenetic analysis of gyrB and rpoD gene sequences showed that P. syringae pv. maculicola, which causes diseases in Brassicaceae, forms six genetic lineages within genomospecies 3 of P. syringae strains as defined by L. Gardan et al. (Int. J. Syst. Bacteriol. 49[Pt 2]:469–478, 1999), whereas P. syringae pv. tomato forms two distinct genetic lineages. A multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) conducted with eight minisatellite loci confirmed the genetic structure obtained with rpoD and gyrB sequence analyses. These results provide promising tools for fine-scale epidemiological studies on diseases caused by P. syringae pv. maculicola and P. syringae pv. tomato. The two pathovars had distinct host ranges; only P. syringae pv. maculicola strains were pathogenic for Brassicaceae. A subpopulation of P. syringae pv. maculicola strains that are pathogenic for Pto-expressing tomato plants were shown to lack avrPto1 and avrPtoB or to contain a disrupted avrPtoB homolog. Taking phylogenetic and pathological features into account, our data suggest that the DC3000 strain belongs to P. syringae pv. maculicola. This study shows that P. syringae pv. maculicola and P. syringae pv. tomato appear multiclonal, as they did not diverge from a single common ancestral group within the ancestral P. syringae genomospecies 3, and suggests that pathovar specificity within P. syringae may be due to independent genetic events. PMID:22389364

  8. Evaluating the impacts of stressors of Pseudomonas syringae pathovar tomato on the effectiveness of multi-locus variable number tandem repeat analysis and multi-locus sequence typing in microbial forensic investigations

    PubMed Central

    2014-01-01

    Background Crops in the USA are vulnerable to natural and criminal threats because of their widespread cultivation and lack of surveillance, and because of implementation of growing practices such as monoculture. To prepare for investigation and attribution of such events, forensic assays, including determination of molecular profiles, are being adapted for use with plant pathogens. The use of multi-locus variable number tandem repeat (VNTR) analysis (MLVA) and multi-locus sequence typing (MLST) in investigations involving plant pathogens may be problematic because the long lag periods between pathogen introduction and discovery of associated disease may provide enough time for evolution to occur in the regions of the genome employed in each assay. Thus, more information on the stability of the loci employed in these methods is needed. Results The MLVA fingerprints and MLST profiles were consistent throughout the experiment, indicating that, using a specific set of primers and conditions, MLVA and MLST typing systems reliably identify P.s. tomato DC3000. This information is essential to forensic investigators in interpreting comparisons between MLVA and MLST typing profiles observed in P.s. tomato isolates. Conclusions Our results indicate that MLVA and MLST typing systems, utilizing the specified primers and conditions, could be employed successfully in forensics investigations involving P.s. tomato. Similar experiments should be conducted in the field and with other high-consequence plant pathogens to ensure that the assays are reliable for pathogens infecting plants in their natural environment and for organisms that may display faster rates of mutation. PMID:25132953

  9. Supplementation of H1N1pdm09 split vaccine with heterologous tandem repeat M2e5x virus-like particles confers improved cross-protection in ferrets.

    PubMed

    Music, Nedzad; Reber, Adrian J; Kim, Min-Chul; York, Ian A; Kang, Sang-Moo

    2016-01-20

    Current influenza vaccines induce strain-specific immunity to the highly variable hemagglutinin (HA) protein. It is therefore a high priority to develop vaccines that induce broadly cross-protective immunity to different strains of influenza. Since influenza A M2 proteins are highly conserved among different strains, five tandem repeats of the extracellular peptide of M2 in a membrane-anchored form on virus-like particles (VLPs) have been suggested to be a promising candidate for universal influenza vaccine. In this study, ferrets were intramuscularly immunized with 2009 H1N1 split HA vaccine ("Split") alone, influenza split vaccine supplemented with M2e5x VLP ("Split+M2e5x"), M2e5x VLP alone ("M2e5x"), or mock immunized. Vaccine efficacy was measured serologically and by protection against a serologically distinct viral challenge. Ferrets immunized with Split+M2e5x induced HA strain specific and conserved M2e immunity. Supplementation of M2e5x VLP to split vaccination significantly increased the immunogenicity of split vaccine compared to split alone. The Split+M2e5x ferret group showed evidence of cross-reactive protection, including faster recovery from weight loss, and reduced inflammation, as inferred from changes in peripheral leukocyte subsets, compared to mock-immunized animals. In addition, ferrets immunized with Split+M2e5x shed lower viral nasal-wash titers than the other groups. Ferrets immunized with M2e5x alone also show some protective effects, while those immunized with split vaccine alone induced no protective effects compared to mock-immunized ferrets. These studies suggest that supplementation of split vaccine with M2e5x-VLP may provide broader and improved cross-protection than split vaccine alone. PMID:26709639

  10. Fuzzy jets

    DOE PAGESBeta

    Mackey, Lester; Nachman, Benjamin; Schwartzman, Ariel; Stansbury, Conrad

    2016-06-01

    Here, collimated streams of particles produced in high energy physics experiments are organized using clustering algorithms to form jets . To construct jets, the experimental collaborations based at the Large Hadron Collider (LHC) primarily use agglomerative hierarchical clustering schemes known as sequential recombination. We propose a new class of algorithms for clustering jets that use infrared and collinear safe mixture models. These new algorithms, known as fuzzy jets , are clustered using maximum likelihood techniques and can dynamically determine various properties of jets like their size. We show that the fuzzy jet size adds additional information to conventional jet taggingmore » variables in boosted topologies. Furthermore, we study the impact of pileup and show that with some slight modifications to the algorithm, fuzzy jets can be stable up to high pileup interaction multiplicities.« less

  11. Fuzzy jets

    NASA Astrophysics Data System (ADS)

    Mackey, Lester; Nachman, Benjamin; Schwartzman, Ariel; Stansbury, Conrad

    2016-06-01

    Collimated streams of particles produced in high energy physics experiments are organized using clustering algorithms to form jets. To construct jets, the experimental collaborations based at the Large Hadron Collider (LHC) primarily use agglomerative hierarchical clustering schemes known as sequential recombination. We propose a new class of algorithms for clustering jets that use infrared and collinear safe mixture models. These new algorithms, known as fuzzy jets, are clustered using maximum likelihood techniques and can dynamically determine various properties of jets like their size. We show that the fuzzy jet size adds additional information to conventional jet tagging variables in boosted topologies. Furthermore, we study the impact of pileup and show that with some slight modifications to the algorithm, fuzzy jets can be stable up to high pileup interaction multiplicities.

  12. Patterns of tandem repetition in plant whole genome assemblies.

    PubMed

    Navajas-Pérez, Rafael; Paterson, Andrew H

    2009-06-01

    Tandem repeats often confound large genome assemblies. A survey of tandemly arrayed repetitive sequences was carried out in whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, and papaya, in order to test how these assemblies deal with this fraction of DNA. Our results suggest that plant genome assemblies preferentially include tandem repeats composed of shorter monomeric units (especially dinucleotide and 9-30-bp repeats), while higher repetitive units pose more difficulties to assemble. Nevertheless, notwithstanding that currently available sequencing technologies struggle with higher arrays of repeated DNA, major well-known repetitive elements including centromeric and telomeric repeats as well as high copy-number genes, were found to be reasonably well represented. A database including all tandem repeat sequences characterized here was created to benefit future comparative genomic analyses. PMID:19242726

  13. Revisiting the TALE repeat.

    PubMed

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity. PMID:24622844

  14. The Pentapeptide Repeat Proteins

    SciTech Connect

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  15. Homologous recombination plays minor role in excision of unit-length viral genomes from head-to-tail direct tandem repeats of porcine circovirus during DNA replication in Escherichia coli

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously, we demonstrated that a theta-replicating bacterial plasmid containing 1.75 copies of genomic porcine circovirus (PCV) DNA in head-to-tail tandem (HTT) [a partial copy of PCV type 1 (PCV1), a complete copy of PCV type 2 (PCV2) and two origins of DNA replication (Ori)] yielded three differ...

  16. Hybrid fuzzy regression with trapezoidal fuzzy data

    NASA Astrophysics Data System (ADS)

    Razzaghnia, T.; Danesh, S.; Maleki, A.

    2011-12-01

    In this regard, this research deals with a method for hybrid fuzzy least-squares regression. The extension of symmetric triangular fuzzy coefficients to asymmetric trapezoidal fuzzy coefficients is considered as an effective measure for removing unnecessary fuzziness of the linear fuzzy model. First, trapezoidal fuzzy variable is applied to derive a bivariate regression model. In the following, normal equations are formulated to solve the four parts of hybrid regression coefficients. Also the model is extended to multiple regression analysis. Eventually, method is compared with Y-H.O. chang's model.

  17. All Repeats are Not Equal: A Module-Based Approach to Guide Repeat Protein Design

    PubMed Central

    Regan, Lynne

    2013-01-01

    Repeat proteins composed of tandem arrays of a short structural motif often mediate protein-protein interactions. Past efforts to design repeat protein-based molecular recognition tools have focused on the creation of templates from the consensus of individual repeats, regardless of their natural context. Such an approach assumes that all repeats are essentially equivalent. In this study we present the results of a ‘module-based’ approach, in which modules composed of tandem repeats are aligned to identify repeat-specific features. Using this approach to analyze tetratricopeptide repeat modules that contain 3 tandem repeats (3TPRs), we identify two classes of 3TPR modules with distinct structural signatures that are correlated with different sets of functional residues. Our analyses also reveal a high degree of correlation between positions across the entire ligand-binding surface, indicative of a coordinated, coevolving binding surface. Extension of our analyses to different repeat protein modules reveals more examples of repeat-specific features, especially in armadillio repeat (ARM) modules. In summary, the module-based analyses that we present effectively capture key repeat-specific features that will be important to include in future repeat protein design templates. PMID:23434848

  18. Fuzzy associative memories

    NASA Technical Reports Server (NTRS)

    Kosko, Bart

    1991-01-01

    Mappings between fuzzy cubes are discussed. This level of abstraction provides a surprising and fruitful alternative to the propositional and predicate-calculas reasoning techniques used in expert systems. It allows one to reason with sets instead of propositions. Discussed here are fuzzy and neural function estimators, neural vs. fuzzy representation of structured knowledge, fuzzy vector-matrix multiplication, and fuzzy associative memory (FAM) system architecture.

  19. Universal Approximation of Mamdani Fuzzy Controllers and Fuzzy Logical Controllers

    NASA Technical Reports Server (NTRS)

    Yuan, Bo; Klir, George J.

    1997-01-01

    In this paper, we first distinguish two types of fuzzy controllers, Mamdani fuzzy controllers and fuzzy logical controllers. Mamdani fuzzy controllers are based on the idea of interpolation while fuzzy logical controllers are based on fuzzy logic in its narrow sense, i.e., fuzzy propositional logic. The two types of fuzzy controllers treat IF-THEN rules differently. In Mamdani fuzzy controllers, rules are treated disjunctively. In fuzzy logic controllers, rules are treated conjunctively. Finally, we provide a unified proof of the property of universal approximation for both types of fuzzy controllers.

  20. Sequence repeats and protein structure

    NASA Astrophysics Data System (ADS)

    Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

    2012-11-01

    Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

  1. Tandem Couture

    PubMed Central

    Ericksen, Spencer S.; Boileau, Andrew J.

    2008-01-01

    Receptor subunits in the Cys-loop superfamily assemble to form channels as homopentamers or heteropentamers, expanding functional diversity through modularity. Expression of two or more compatible subunit types can lead to various receptor assemblies or subtypes. However, what may be good for diversity in vivo may be undesirable for the bench scientist, because we often wish to reduce our analyses to a single receptor subtype. By linking two or more subunits, creating tandems or concatamers, we can control stoichiometry and limit expression to exactly one receptor subtype. In this fashion, receptors with mixed subunit subtypes and heterozygous mutations can be separated from a mixture and can be described in detail. However, several recent studies have shown that this may be more easily conceived than accomplished, because several unforeseen problems have arisen. Concatamers can degrade, linkers can sometimes be clipped after or during translation, and one subunit may “loop out” or even become part of a second (now linked) pentamer with different characteristics. Some strategies have been developed to overcome these drawbacks, and the resultant new information that has begun to emerge has revitalized the study of these receptors in heterologous expression systems. PMID:17519509

  2. Fuzzy logic controller optimization

    DOEpatents

    Sepe, Jr., Raymond B; Miller, John Michael

    2004-03-23

    A method is provided for optimizing a rotating induction machine system fuzzy logic controller. The fuzzy logic controller has at least one input and at least one output. Each input accepts a machine system operating parameter. Each output produces at least one machine system control parameter. The fuzzy logic controller generates each output based on at least one input and on fuzzy logic decision parameters. Optimization begins by obtaining a set of data relating each control parameter to at least one operating parameter for each machine operating region. A model is constructed for each machine operating region based on the machine operating region data obtained. The fuzzy logic controller is simulated with at least one created model in a feedback loop from a fuzzy logic output to a fuzzy logic input. Fuzzy logic decision parameters are optimized based on the simulation.

  3. Fuzzy slope stability method

    SciTech Connect

    Kacewicz, M.

    1987-11-01

    An approach for the description of uncertainty in geology using fuzzy-set theory and an example of slope stability problem is presented. Soil parameters may be described by fuzzy sets. The fuzzy method of slope stability estimation is considered and verified in the case of one of Warsaw's (Poland) slopes.

  4. Fuzzy Logic Engine

    NASA Technical Reports Server (NTRS)

    Howard, Ayanna

    2005-01-01

    The Fuzzy Logic Engine is a software package that enables users to embed fuzzy-logic modules into their application programs. Fuzzy logic is useful as a means of formulating human expert knowledge and translating it into software to solve problems. Fuzzy logic provides flexibility for modeling relationships between input and output information and is distinguished by its robustness with respect to noise and variations in system parameters. In addition, linguistic fuzzy sets and conditional statements allow systems to make decisions based on imprecise and incomplete information. The user of the Fuzzy Logic Engine need not be an expert in fuzzy logic: it suffices to have a basic understanding of how linguistic rules can be applied to the user's problem. The Fuzzy Logic Engine is divided into two modules: (1) a graphical-interface software tool for creating linguistic fuzzy sets and conditional statements and (2) a fuzzy-logic software library for embedding fuzzy processing capability into current application programs. The graphical- interface tool was developed using the Tcl/Tk programming language. The fuzzy-logic software library was written in the C programming language.

  5. Applications of fuzzy logic

    SciTech Connect

    Zargham, M.R.

    1995-06-01

    Recently, fuzzy logic has been applied to many areas, such as process control, image understanding, robots, expert systems, and decision support systems. This paper will explain the basic concepts of fuzzy logic and its application in different fields. The steps to design a control system will be explained in detail. Fuzzy control is the first successful industrial application of fuzzy logic. A fuzzy controller is able to control systems which previously could only be controlled by skilled operators. In recent years Japan has achieved significant progress in this area and has applied it to variety of products such as cruise control for cars, video cameras, rice cookers, washing machines, etc.

  6. Recurrent fuzzy ranking methods

    NASA Astrophysics Data System (ADS)

    Hajjari, Tayebeh

    2012-11-01

    With the increasing development of fuzzy set theory in various scientific fields and the need to compare fuzzy numbers in different areas. Therefore, Ranking of fuzzy numbers plays a very important role in linguistic decision-making, engineering, business and some other fuzzy application systems. Several strategies have been proposed for ranking of fuzzy numbers. Each of these techniques has been shown to produce non-intuitive results in certain case. In this paper, we reviewed some recent ranking methods, which will be useful for the researchers who are interested in this area.

  7. Fuzzy Sets and Mathematical Education.

    ERIC Educational Resources Information Center

    Alsina, C.; Trillas, E.

    1991-01-01

    Presents the concept of "Fuzzy Sets" and gives some ideas for its potential interest in mathematics education. Defines what a Fuzzy Set is, describes why we need to teach fuzziness, gives some examples of fuzzy questions, and offers some examples of activities related to fuzzy sets. (MDH)

  8. Repeating thermocouple

    SciTech Connect

    Falk, R. A.

    1985-06-04

    Disclosed herein is a repeating use thermocouple assembly and method of making the same in which a cavity adjacent the tip of the thermocouple is filled with a thermosetting foundry sand and baked in place to provide support for the thermocouple tube without causing stresses during use which could cause breakage of the thermocouple tube.

  9. Introduction to Fuzzy Set Theory

    NASA Technical Reports Server (NTRS)

    Kosko, Bart

    1990-01-01

    An introduction to fuzzy set theory is described. Topics covered include: neural networks and fuzzy systems; the dynamical systems approach to machine intelligence; intelligent behavior as adaptive model-free estimation; fuzziness versus probability; fuzzy sets; the entropy-subsethood theorem; adaptive fuzzy systems for backing up a truck-and-trailer; product-space clustering with differential competitive learning; and adaptive fuzzy system for target tracking.

  10. System Using Tandem Repeats of the cA Peptidoglycan-Binding Domain from Lactococcus lactis for Display of both N- and C-Terminal Fusions on Cell Surfaces of Lactic Acid Bacteria▿

    PubMed Central

    Okano, Kenji; Zhang, Qiao; Kimura, Sakurako; Narita, Junya; Tanaka, Tsutomu; Fukuda, Hideki; Kondo, Akihiko

    2008-01-01

    Here, we established a system for displaying heterologous protein to the C terminus of the peptidoglycan-binding domain (cA domain) of AcmA (a major autolysin from Lactococcus lactis). Western blot and flow cytometric analyses revealed that the fusion proteins (cA-AmyA) of the cA domain and α-amylase from Streptococcus bovis 148 (AmyA) are efficiently expressed and successfully displayed on the surfaces of L. lactis cells. AmyA was also displayed on the cell surface while retaining its activity. Moreover, with an increase in the number of cA domains, the quantity of cA-AmyA fusion proteins displayed on the cell surface increased. When three repeats of the cA domain were used as an anchor protein, 82% of α-amylase activity was detected on the cells. The raw starch-degrading activity of AmyA was significantly higher when AmyA was fused to the C terminus of the cA domain than when it was fused to the N terminus. In addition, cA-AmyA fusion proteins were successfully displayed on the cell surfaces of Lactobacillus plantarum and Lactobacillus casei. PMID:18156338

  11. System using tandem repeats of the cA peptidoglycan-binding domain from Lactococcus lactis for display of both N- and C-terminal fusions on cell surfaces of lactic acid bacteria.

    PubMed

    Okano, Kenji; Zhang, Qiao; Kimura, Sakurako; Narita, Junya; Tanaka, Tsutomu; Fukuda, Hideki; Kondo, Akihiko

    2008-02-01

    Here, we established a system for displaying heterologous protein to the C terminus of the peptidoglycan-binding domain (cA domain) of AcmA (a major autolysin from Lactococcus lactis). Western blot and flow cytometric analyses revealed that the fusion proteins (cA-AmyA) of the cA domain and alpha-amylase from Streptococcus bovis 148 (AmyA) are efficiently expressed and successfully displayed on the surfaces of L. lactis cells. AmyA was also displayed on the cell surface while retaining its activity. Moreover, with an increase in the number of cA domains, the quantity of cA-AmyA fusion proteins displayed on the cell surface increased. When three repeats of the cA domain were used as an anchor protein, 82% of alpha-amylase activity was detected on the cells. The raw starch-degrading activity of AmyA was significantly higher when AmyA was fused to the C terminus of the cA domain than when it was fused to the N terminus. In addition, cA-AmyA fusion proteins were successfully displayed on the cell surfaces of Lactobacillus plantarum and Lactobacillus casei. PMID:18156338

  12. Fuzzy mathematical techniques with applications

    SciTech Connect

    Kandel, A.

    1986-01-01

    This text presents the basic concepts of fuzzy set theory within a context of real-world applications. The book is self-contained and can be used as a starting point for people interested in this fast growing field as well as by researchers looking for new application techniques. The section on applications includes: Manipulation of knowledge in expert systems; relational database structures; pattern clustering; analysis of transient behavior in digital systems; modeling of uncertainty and search trees. Contents: Fuzzy sets; Possibility theory and fuzzy quantification; Fuzzy functions; Fuzzy events and fuzzy statistics; Fuzzy relations; Fuzzy logics; Some applications; Bibliography.

  13. Fuzzy and neural control

    NASA Technical Reports Server (NTRS)

    Berenji, Hamid R.

    1992-01-01

    Fuzzy logic and neural networks provide new methods for designing control systems. Fuzzy logic controllers do not require a complete analytical model of a dynamic system and can provide knowledge-based heuristic controllers for ill-defined and complex systems. Neural networks can be used for learning control. In this chapter, we discuss hybrid methods using fuzzy logic and neural networks which can start with an approximate control knowledge base and refine it through reinforcement learning.

  14. Some Properties of Fuzzy Soft Proximity Spaces

    PubMed Central

    Demir, İzzettin; Özbakır, Oya Bedre

    2015-01-01

    We study the fuzzy soft proximity spaces in Katsaras's sense. First, we show how a fuzzy soft topology is derived from a fuzzy soft proximity. Also, we define the notion of fuzzy soft δ-neighborhood in the fuzzy soft proximity space which offers an alternative approach to the study of fuzzy soft proximity spaces. Later, we obtain the initial fuzzy soft proximity determined by a family of fuzzy soft proximities. Finally, we investigate relationship between fuzzy soft proximities and proximities. PMID:25793224

  15. GENETIC DIVERSITY OF TYPHA LATIFOLIA (TYPHACEAE) AND THE IMPACT OF POLLUTANTS EXAMINED WITH TANDEM-REPETITIVE DNA PROBES

    EPA Science Inventory

    Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated "core" sequences (GACA, GATA, and GCAC). The principal objectives of this investigation w...

  16. Clustering by Fuzzy Neural Gas and Evaluation of Fuzzy Clusters

    PubMed Central

    Geweniger, Tina; Fischer, Lydia; Kaden, Marika; Lange, Mandy; Villmann, Thomas

    2013-01-01

    We consider some modifications of the neural gas algorithm. First, fuzzy assignments as known from fuzzy c-means and neighborhood cooperativeness as known from self-organizing maps and neural gas are combined to obtain a basic Fuzzy Neural Gas. Further, a kernel variant and a simulated annealing approach are derived. Finally, we introduce a fuzzy extension of the ConnIndex to obtain an evaluation measure for clusterings based on fuzzy vector quantization. PMID:24396342

  17. Simplify fuzzy control implementation

    SciTech Connect

    Stoll, K.E.; Ralston, P.A.S.; Ramaganesan, S. )

    1993-07-01

    A controller that uses fuzzy rules provides better response than a conventional linear controller in some applications. The rules are best implemented as a breakpoint function. A level control example illustrates the technique and advantages over proportional-integral (PI) control. In numerous papers on fuzzy controller development, emphasis has been primarily on formal inferencing, membership functions, and steps in building a fuzzy relation, as described by Zadeh. The rationale used in formulating the required set of rules is usually neglected, and the interpretation of the final controller as an input-output algorithm is overlooked. Also, the details of fuzzy mathematics are unfamiliar to many engineers and the implementation appears cumbersome to most. Process description and control instrumentation. This article compares a fuzzy controller designed by specifying a breakpoint function with a traditional PI controller for a level control system on a laboratory scale. In this discussion, only setpoint changes are considered.

  18. Pentapeptide Repeat Proteins and Cyanobacteria

    SciTech Connect

    Buchko, Garry W.

    2009-10-16

    Cyanobacteria are unique in many ways and one unusual feature is the presence of a suite of proteins that contain at least one domain with a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. The function of such pentapeptide repeat proteins (PRPs) are still unknown, however, their prevalence in cyanobacteria suggests that they may play some role in the unique biological activities of cyanobacteria. As part of an inter-disciplinary Membrane Biology Grand Challenge at the Environmental Molecular Sciences Laboratory (Pacific Northwest National Laboratory) and Washington University in St. Louis, the genome of Cyanothece 51142 was sequenced and its molecular biology studied with relation to circadian rhythms. The genome of Cyanothece encodes for 35 proteins that contain at least one PRP domain. These proteins range in size from 105 (Cce_3102) to 930 (Cce_2929) kDa with the PRP domains ranging in predicted size from 12 (Cce_1545) to 62 (cce_3979) tandem pentapeptide repeats. Transcriptomic studies with 29 out of the 35 genes showed that at least three of the PRPs in Cyanothece 51142 (cce_0029, cce_3083, and cce_3272) oscillated with repeated periods of light and dark, further supporting a biological function for PRPs. Using X-ray diffraction crystallography, the structure for two pentapeptide repeat proteins from Cyanothece 51142 were determined, cce_1272 (aka Rfr32) and cce_4529 (aka Rfr23). Analysis of their molecular structures suggests that all PRP may share the same structural motif, a novel type of right-handed quadrilateral β-helix, or Rfr-fold, reminiscent of a square tower with four distinct faces. Each pentapeptide repeat occupies one face of the Rfr-fold with four consecutive pentapeptide repeats completing a coil that, in turn, stack upon each other to form “protein skyscrapers”. Details of the structural features of the Rfr-fold are reviewed here together with a discussion for the possible role of end

  19. Tandem mobile robot system

    DOEpatents

    Buttz, James H.; Shirey, David L.; Hayward, David R.

    2003-01-01

    A robotic vehicle system for terrain navigation mobility provides a way to climb stairs, cross crevices, and navigate across difficult terrain by coupling two or more mobile robots with a coupling device and controlling the robots cooperatively in tandem.

  20. Comparison of seven techniques for typing international epidemic strains of Clostridium difficile: restriction endonuclease analysis, pulsed-field gel electrophoresis, PCR-ribotyping, multilocus sequence typing, multilocus variable-number tandem-repeat analysis, amplified fragment length polymorphism, and surface layer protein A gene sequence typing.

    PubMed

    Killgore, George; Thompson, Angela; Johnson, Stuart; Brazier, Jon; Kuijper, Ed; Pepin, Jacques; Frost, Eric H; Savelkoul, Paul; Nicholson, Brad; van den Berg, Renate J; Kato, Haru; Sambol, Susan P; Zukowski, Walter; Woods, Christopher; Limbago, Brandi; Gerding, Dale N; McDonald, L Clifford

    2008-02-01

    Using 42 isolates contributed by laboratories in Canada, The Netherlands, the United Kingdom, and the United States, we compared the results of analyses done with seven Clostridium difficile typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing (slpAST), PCR-ribotyping, restriction endonuclease analysis (REA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). We assessed the discriminating ability and typeability of each technique as well as the agreement among techniques in grouping isolates by allele profile A (AP-A) through AP-F, which are defined by toxinotype, the presence of the binary toxin gene, and deletion in the tcdC gene. We found that all isolates were typeable by all techniques and that discrimination index scores for the techniques tested ranged from 0.964 to 0.631 in the following order: MLVA, REA, PFGE, slpAST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain of C. difficile (BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and no tcdC gene deletion). REA, slpAST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion in tcdC) in a single group that excluded other APs. PFGE, AFLP, and MLVA grouped two, one, and two different non-AP-B isolates, respectively, with their AP-B isolates. All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks. PMID:18039796

  1. Fuzzy blood pressure measurement

    NASA Astrophysics Data System (ADS)

    Cuce, Antonino; Di Guardo, Mario; Sicurella, Gaetano

    1998-10-01

    In this paper, an intelligent system for blood pressure measurement is posed together with a possible implementation using an eight bit fuzzy processor. The system can automatically determine the ideal cuff inflation level eliminating the discomfort and misreading caused by incorrect cuff inflation. Using statistics distribution of the systolic and diastolic blood pressure, in the inflation phase, a fuzzy rule system determine the pressure levels at which checking the presence of heart beat in order to exceed the systolic pressure with the minimum gap. The heart beats, characterized through pressure variations, are recognized by a fuzzy classifier.

  2. Complex intuitionistic fuzzy sets

    NASA Astrophysics Data System (ADS)

    Alkouri, Abdulazeez (Moh'd. Jumah) S.; Salleh, Abdul Razak

    2012-09-01

    This paper presents a new concept of complex intuitionistic fuzzy set (CIFS) which is generalized from the innovative concept of a complex fuzzy set (CFS) by adding the non-membership term to the definition of CFS. The novelty of CIFS lies in its ability for membership and non-membership functions to achieve more range of values. The ranges of values are extended to the unit circle in complex plane for both membership and non-membership functions instead of [0, 1] as in the conventional intuitionistic fuzzy functions. We define basic operations namely complement, union, and intersection on CIFSs. Properties of these operations are derived.

  3. Fuzziness in abacus logic

    NASA Astrophysics Data System (ADS)

    Malhas, Othman Qasim

    1993-10-01

    The concept of “abacus logic” has recently been developed by the author (Malhas, n.d.). In this paper the relation of abacus logic to the concept of fuzziness is explored. It is shown that if a certain “regularity” condition is met, concepts from fuzzy set theory arise naturally within abacus logics. In particular it is shown that every abacus logic then has a “pre-Zadeh orthocomplementation”. It is also shown that it is then possible to associate a fuzzy set with every proposition of abacus logic and that the collection of all such sets satisfies natural conditions expected in systems of fuzzy logic. Finally, the relevance to quantum mechanics is discussed.

  4. Fuzzy Risk Analyzer

    Energy Science and Technology Software Center (ESTSC)

    1994-03-04

    FRA is a general purpose code for risk analysis using fuzzy, not numeric, attributes. It allows the user to evaluate the risk associated with a composite system on the basis of the risk estimates of the individual components.

  5. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants.

    PubMed

    Sharma, Manisha; Pandey, Girdhar K

    2015-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  6. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants

    PubMed Central

    Sharma, Manisha; Pandey, Girdhar K.

    2016-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein–protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  7. Tandem Air Propellers - II

    NASA Technical Reports Server (NTRS)

    Lesley, E. P.

    1939-01-01

    Tests of three-blade, adjustable-pitch counterrotating tandem model propellers, adjusted to absorb equal power at maximum efficiency of the combination, were made at Stanford University. The aerodynamic characteristics, for blade-angle settings of 15, 25, 35, 45, 55, and 65 degrees at 0.75R of the forward propeller and for diameters spacings of 8-1/2, 15 and 30% were compared with those of three-blade and six-blade propellers of the same blade form. It was found that, in order to realize the condition of equal power at maximum efficiency, the blade angles for the rear propeller must be generally less than for the forward propeller, the difference increasing the blade angle. The tests showed that, at maximum efficiency, the tandem propellers absorb about double the power of three-blade propellers and about 8% more power than six-blade propellers having the pitch of the forward propeller of the tandem combination. The maximum efficiency of the tandem propellers was found to be from 2-15% greater than for six-blade propellers, the difference varying directly with blade angle. It was also found that the maximum efficiency of the tandem propellers was greater than that of a three-blade propeller for blade angles at 0.75R of 25 degrees or more. The difference in maximum efficiency again varied directly with blade angle, being about 9% for 65 degrees at 0.75R.

  8. Fuzzy control of magnetic bearings

    NASA Technical Reports Server (NTRS)

    Feeley, J. J.; Niederauer, G. M.; Ahlstrom, D. J.

    1991-01-01

    The use of an adaptive fuzzy control algorithm implemented on a VLSI chip for the control of a magnetic bearing was considered. The architecture of the adaptive fuzzy controller is similar to that of a neural network. The performance of the fuzzy controller is compared to that of a conventional controller by computer simulation.

  9. Component Models for Fuzzy Data

    ERIC Educational Resources Information Center

    Coppi, Renato; Giordani, Paolo; D'Urso, Pierpaolo

    2006-01-01

    The fuzzy perspective in statistical analysis is first illustrated with reference to the "Informational Paradigm" allowing us to deal with different types of uncertainties related to the various informational ingredients (data, model, assumptions). The fuzzy empirical data are then introduced, referring to "J" LR fuzzy variables as observed on "I"…

  10. An approximation of interval type-2 fuzzy controllers using fuzzy ratio switching type-1 fuzzy controllers.

    PubMed

    Tao, C W; Taur, Jinshiuh; Chuang, Chen-Chia; Chang, Chia-Wen; Chang, Yeong-Hwa

    2011-06-01

    In this paper, the interval type-2 fuzzy controllers (FC(IT2)s) are approximated using the fuzzy ratio switching type-1 FCs to avoid the complex type-reduction process required for the interval type-2 FCs. The fuzzy ratio switching type-1 FCs (FC(FRST1)s) are designed to be a fuzzy combination of the possible-leftmost and possible-rightmost type-1 FCs. The fuzzy ratio switching type-1 fuzzy control technique is applied with the sliding control technique to realize the hybrid fuzzy ratio switching type-1 fuzzy sliding controllers (HFSC(FRST1)s) for the double-pendulum-and-cart system. The simulation results and comparisons with other approaches are provided to demonstrate the effectiveness of the proposed HFSC(FRST1)s. PMID:21189244

  11. Solving fuzzy polynomial equation and the dual fuzzy polynomial equation using the ranking method

    NASA Astrophysics Data System (ADS)

    Rahman, Nurhakimah Ab.; Abdullah, Lazim

    2014-06-01

    Fuzzy polynomials with trapezoidal and triangular fuzzy numbers have attracted interest among some researchers. Many studies have been done by researchers to obtain real roots of fuzzy polynomials. As a result, there are many numerical methods involved in obtaining the real roots of fuzzy polynomials. In this study, we will present the solution to the fuzzy polynomial equation and dual fuzzy polynomial equation using the ranking method of fuzzy numbers and subsequently transforming fuzzy polynomials to crisp polynomials. This transformation is performed using the ranking method based on three parameters, namely Value, Ambiguity and Fuzziness. Finally, we illustrate our approach with two numerical examples for fuzzy polynomial equation and dual fuzzy polynomial equation.

  12. A neural fuzzy controller learning by fuzzy error propagation

    NASA Technical Reports Server (NTRS)

    Nauck, Detlef; Kruse, Rudolf

    1992-01-01

    In this paper, we describe a procedure to integrate techniques for the adaptation of membership functions in a linguistic variable based fuzzy control environment by using neural network learning principles. This is an extension to our work. We solve this problem by defining a fuzzy error that is propagated back through the architecture of our fuzzy controller. According to this fuzzy error and the strength of its antecedent each fuzzy rule determines its amount of error. Depending on the current state of the controlled system and the control action derived from the conclusion, each rule tunes the membership functions of its antecedent and its conclusion. By this we get an unsupervised learning technique that enables a fuzzy controller to adapt to a control task by knowing just about the global state and the fuzzy error.

  13. Tandem mirror fusion research

    SciTech Connect

    Baldwin, D.E.

    1983-12-02

    The tandem mirror program has evolved considerably in the last decade. Of significance is the viable reactor concept embodied in the MARS design. An aggressive experimental program, culminating in the operation of MFTF-B in late 1986, will provide a firm basis for refining the MARS design as necessary for constructing a reactor prototype in the 1990s.

  14. Reconfigurable fuzzy cell

    NASA Technical Reports Server (NTRS)

    Salazar, George A. (Inventor)

    1993-01-01

    This invention relates to a reconfigurable fuzzy cell comprising a digital control programmable gain operation amplifier, an analog-to-digital converter, an electrically erasable PROM, and 8-bit counter and comparator, and supporting logic configured to achieve in real-time fuzzy systems high throughput, grade-of-membership or membership-value conversion of multi-input sensor data. The invention provides a flexible multiplexing-capable configuration, implemented entirely in hardware, for effectuating S-, Z-, and PI-membership functions or combinations thereof, based upon fuzzy logic level-set theory. A membership value table storing 'knowledge data' for each of S-, Z-, and PI-functions is contained within a nonvolatile memory for storing bits of membership and parametric information in a plurality of address spaces. Based upon parametric and control signals, analog sensor data is digitized and converted into grade-of-membership data. In situ learn and recognition modes of operation are also provided.

  15. Fuzzy object modeling

    NASA Astrophysics Data System (ADS)

    Udupa, Jayaram K.; Odhner, Dewey; Falcao, Alexandre X.; Ciesielski, Krzysztof C.; Miranda, Paulo A. V.; Vaideeswaran, Pavithra; Mishra, Shipra; Grevera, George J.; Saboury, Babak; Torigian, Drew A.

    2011-03-01

    To make Quantitative Radiology (QR) a reality in routine clinical practice, computerized automatic anatomy recognition (AAR) becomes essential. As part of this larger goal, we present in this paper a novel fuzzy strategy for building bodywide group-wise anatomic models. They have the potential to handle uncertainties and variability in anatomy naturally and to be integrated with the fuzzy connectedness framework for image segmentation. Our approach is to build a family of models, called the Virtual Quantitative Human, representing normal adult subjects at a chosen resolution of the population variables (gender, age). Models are represented hierarchically, the descendents representing organs contained in parent organs. Based on an index of fuzziness of the models, 32 thorax data sets, and 10 organs defined in them, we found that the hierarchical approach to modeling can effectively handle the non-linear relationships in position, scale, and orientation that exist among organs in different patients.

  16. Diversity and evolution of centromere repeats in the maize genome.

    PubMed

    Bilinski, Paul; Distor, Kevin; Gutierrez-Lopez, Jose; Mendoza, Gabriela Mendoza; Shi, Jinghua; Dawe, R Kelly; Ross-Ibarra, Jeffrey

    2015-03-01

    Centromere repeats are found in most eukaryotes and play a critical role in kinetochore formation. Though centromere repeats exhibit considerable diversity both within and among species, little is understood about the mechanisms that drive centromere repeat evolution. Here, we use maize as a model to investigate how a complex history involving polyploidy, fractionation, and recent domestication has impacted the diversity of the maize centromeric repeat CentC. We first validate the existence of long tandem arrays of repeats in maize and other taxa in the genus Zea. Although we find considerable sequence diversity among CentC copies genome-wide, genetic similarity among repeats is highest within these arrays, suggesting that tandem duplications are the primary mechanism for the generation of new copies. Nonetheless, clustering analyses identify similar sequences among distant repeats, and simulations suggest that this pattern may be due to homoplasious mutation. Although the two ancestral subgenomes of maize have contributed nearly equal numbers of centromeres, our analysis shows that the majority of all CentC repeats derive from one of the parental genomes, with an even stronger bias when examining the largest assembled contiguous clusters. Finally, by comparing maize with its wild progenitor teosinte, we find that the abundance of CentC likely decreased after domestication, while the pericentromeric repeat Cent4 has drastically increased. PMID:25190528

  17. Tandem resonator reflectance modulator

    DOEpatents

    Fritz, Ian J.; Wendt, Joel R.

    1994-01-01

    A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors.

  18. Tandem resonator reflectance modulator

    DOEpatents

    Fritz, I.J.; Wendt, J.R.

    1994-09-06

    A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors. 8 figs.

  19. Fast Fuzzy Arithmetic Operations

    NASA Technical Reports Server (NTRS)

    Hampton, Michael; Kosheleva, Olga

    1997-01-01

    In engineering applications of fuzzy logic, the main goal is not to simulate the way the experts really think, but to come up with a good engineering solution that would (ideally) be better than the expert's control, In such applications, it makes perfect sense to restrict ourselves to simplified approximate expressions for membership functions. If we need to perform arithmetic operations with the resulting fuzzy numbers, then we can use simple and fast algorithms that are known for operations with simple membership functions. In other applications, especially the ones that are related to humanities, simulating experts is one of the main goals. In such applications, we must use membership functions that capture every nuance of the expert's opinion; these functions are therefore complicated, and fuzzy arithmetic operations with the corresponding fuzzy numbers become a computational problem. In this paper, we design a new algorithm for performing such operations. This algorithm is applicable in the case when negative logarithms - log(u(x)) of membership functions u(x) are convex, and reduces computation time from O(n(exp 2))to O(n log(n)) (where n is the number of points x at which we know the membership functions u(x)).

  20. Fuzziness at the horizon

    NASA Astrophysics Data System (ADS)

    Batic, Davide; Nicolini, Piero

    2010-08-01

    We study the stability of the noncommutative Schwarzschild black hole interior by analysing the propagation of a massless scalar field between the two horizons. We show that the spacetime fuzziness triggered by the field higher momenta can cure the classical exponential blue-shift divergence, suppressing the emergence of infinite energy density in a region nearby the Cauchy horizon.

  1. Tandem betatron accelerator

    NASA Astrophysics Data System (ADS)

    Keinigs, Rhon K.

    1991-04-01

    1407_50The tandem betatron is a compact, high-current induction accelerator that has the capability to accelerate electrons to an energy of order one gigavolt. Based upon the operating principle of a conventional betatron, the tandem betatron employs two synchronized induction cores operating 180 degrees out of phase. Embedded within the cores are the vacuum chambers, and these are connected by linear transport sections to allow for moving the beam back and forth between the two betatrons. The 180 degree phase shift between the core fluxes permits the circumvention of the flux swing constraint that limits the maximum energy gain of a conventional betatron. By transporting the beam between the synchronized cores, an electron can access more than one acceleration cycle, and thereby continue to gain energy. This added degree of freedom also permits a significant decrease in the size of the magnet system. Biasing coils provide independent control of the confining magnetic field. Provided that efficient beam switching can be performed, it appears feasible that a one gigavolt electron beam can be generated and confined. At this energy, a high current electron beam circulating in a one meter radius orbit could provide a very intense source of short wavelength ((lambda) < 10 nm) synchrotron radiation. This has direct application to the emerging field of x-ray lithography. At more modest energies (10 MeV-30 MeV) a compact tandem betatron could be employed in the fields of medical radiation therapy, industrial radiography, and materials processing.

  2. Fuzzy logic in control systems: Fuzzy logic controller. I, II

    NASA Technical Reports Server (NTRS)

    Lee, Chuen Chien

    1990-01-01

    Recent advances in the theory and applications of fuzzy-logic controllers (FLCs) are examined in an analytical review. The fundamental principles of fuzzy sets and fuzzy logic are recalled; the basic FLC components (fuzzification and defuzzification interfaces, knowledge base, and decision-making logic) are described; and the advantages of FLCs for incorporating expert knowledge into a control system are indicated. Particular attention is given to fuzzy implication functions, the interpretation of sentence connectives (and, also), compositional operators, and inference mechanisms. Applications discussed include the FLC-guided automobile developed by Sugeno and Nishida (1985), FLC hardware systems, FLCs for subway trains and ship-loading cranes, fuzzy-logic chips, and fuzzy computers.

  3. Interval-valued fuzzy hypergraph and fuzzy partition.

    PubMed

    Chen, S M

    1997-01-01

    This paper extends the work of H. Lee-Kwang and L.M. Lee (1995) to present the concept of the interval-valued fuzzy hypergraph. In the interval-valued fuzzy hypergraph, the concepts of the dual interval-valued fuzzy hypergraph, the crisp-valued alpha-cut hypergraph, and the interval-valued [alpha(1),alpha(2 )]-cut at beta level hypergraph are developed, where alphain [0, 1], 0fuzzy partition of a system. PMID:18255914

  4. Enantioselective tandem reaction over a site-isolated bifunctional catalyst.

    PubMed

    Xu, Jianyou; Cheng, Tanyu; Zhang, Kun; Wang, Ziyun; Liu, Guohua

    2016-05-21

    Construction of a site-isolated heterogeneous catalyst to realize the compatibility of bimetallic complexes for a feasible tandem reaction is a significant challenge in heterogeneous asymmetric catalysis. Herein, taking advantage of yolk-shell-structured mesoporous silica, we assemble an active site-isolated bifunctional catalyst through assembly of organopalladium-functionality into silicate channels as an outer shell and chiral organoruthenium-functionality onto silicate yolk as an inner core, realizing the one-pot enantioselective tandem reaction from Pd-catalyzed Sonogashira coupling to Ru-catalyzed asymmetric transfer hydrogenation. As presented in this study, this tandem Sonogashira coupling-asymmetric transfer hydrogenation of haloacetophenones and arylacetylenes affords various chiral conjugated alkynols with high yields and up to 99% enantioselectivity. Moreover, a catalyst can also be recovered easily and recycled repeatedly, making it an interesting feature in a practical organic transformation. PMID:27063335

  5. Fuzzy logic particle tracking velocimetry

    NASA Technical Reports Server (NTRS)

    Wernet, Mark P.

    1993-01-01

    Fuzzy logic has proven to be a simple and robust method for process control. Instead of requiring a complex model of the system, a user defined rule base is used to control the process. In this paper the principles of fuzzy logic control are applied to Particle Tracking Velocimetry (PTV). Two frames of digitally recorded, single exposure particle imagery are used as input. The fuzzy processor uses the local particle displacement information to determine the correct particle tracks. Fuzzy PTV is an improvement over traditional PTV techniques which typically require a sequence (greater than 2) of image frames for accurately tracking particles. The fuzzy processor executes in software on a PC without the use of specialized array or fuzzy logic processors. A pair of sample input images with roughly 300 particle images each, results in more than 200 velocity vectors in under 8 seconds of processing time.

  6. A fuzzy-split range control system applied to a fermentation process.

    PubMed

    Fonseca, Rodolpho Rodrigues; Schmitz, Jones Erni; Fileti, Ana Maria Frattini; da Silva, Flavio Vasconcelos

    2013-08-01

    In this study it was proposed the application of a fuzzy-PI controller in tandem with a split range control strategy to regulate the temperature inside a fermentation vat. Simulations were carried out using different configurations of fuzzy controllers and split range combinations for regulatory control. The performance of these control systems were compared using conventional integral of error criteria, the demand of utilities and the control effort. The proposed control system proved able to adequately regulate the temperature in all the tests. Besides, considering a similar ITAE index and using the energetically most efficient split range configuration, fuzzy-PI controller provided a reduction of approximately 84.5% in the control effort and of 6.75% in total demand of utilities by comparison to a conventional PI controller. PMID:23759431

  7. Monolithic tandem solar cell

    DOEpatents

    Wanlass, M.W.

    1994-06-21

    A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. 9 figs.

  8. Monolithic tandem solar cell

    DOEpatents

    Wanlass, Mark W.

    1991-01-01

    A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, and (c) a second photoactive subcell on the first subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. The solar cell can be provided as a two-terminal device or a three-terminal device.

  9. Fuzzy learning under and about an unfamiliar fuzzy teacher

    NASA Technical Reports Server (NTRS)

    Dasarathy, Belur V.

    1992-01-01

    This study addresses the problem of optimal parametric learning in unfamiliar fuzzy environments. Prior studies in the domain of unfamiliar environments, which employed either crisp or fuzzy approaches to model the uncertainty or imperfectness of the learning environment, assumed that the training sample labels provided by the unfamiliar teacher were crisp, even if not perfect. Here, the more realistic problem of fuzzy learning under an unfamiliar teacher who provides only fuzzy (instead of crisp) labels, is tackled by expanding the previously defined fuzzy membership concepts to include an additional component representative of the fuzziness of the teacher. The previously studied scenarios, namely, crisp and fuzzy learning under (crisp) unfamiliar teacher, can be looked upon as special cases of this new methodology. As under the earlier studies, the estimated membership functions can then be deployed during the ensuing classification decision phase to judiciously take into account the imperfectness of the learning environment. The study also offers some insight into the properties of several of these fuzzy membership function estimators by examining their behavior under certain specific scenarios.

  10. Repeated Course Enrollments.

    ERIC Educational Resources Information Center

    Windham, Patricia

    This report resents tables of repeated course enrollment data in Florida community colleges for the fall 1993 cohort. Overall, the percent of repeats in college preparatory courses was greater than that of college credit courses. Within ICS codes, the highest percentage of credit repeat enrollments was in mathematics; the second highest was in…

  11. Comparative study of a learning fuzzy PID controller and a self-tuning controller.

    PubMed

    Kazemian, H B

    2001-01-01

    The self-organising fuzzy controller is an extension of the rule-based fuzzy controller with an additional learning capability. The self-organising fuzzy (SOF) is used as a master controller to readjust conventional PID gains at the actuator level during the system operation, copying the experience of a human operator. The application of the self-organising fuzzy PID (SOF-PID) controller to a 2-link non-linear revolute-joint robot-arm is studied using path tracking trajectories at the setpoint. For the purpose of comparison, the same experiments are repeated by using the self-tuning controller subject to the same data supplied at the setpoint. For the path tracking experiments, the output trajectories of the SOF-PID controller followed the specified path closer and smoother than the self-tuning controller. PMID:11515942

  12. Fuzzy Logic in Medicine and Bioinformatics

    PubMed Central

    Torres, Angela; Nieto, Juan J.

    2006-01-01

    The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions) and in bioinformatics (comparison of genomes). PMID:16883057

  13. On fuzzy ideals of BL-algebras.

    PubMed

    Meng, Biao Long; Xin, Xiao Long

    2014-01-01

    In this paper we investigate further properties of fuzzy ideals of a BL-algebra. The notions of fuzzy prime ideals, fuzzy irreducible ideals, and fuzzy Gödel ideals of a BL-algebra are introduced and their several properties are investigated. We give a procedure to generate a fuzzy ideal by a fuzzy set. We prove that every fuzzy irreducible ideal is a fuzzy prime ideal but a fuzzy prime ideal may not be a fuzzy irreducible ideal and prove that a fuzzy prime ideal ω is a fuzzy irreducible ideal if and only if ω(0) = 1 and |Im(ω)| = 2. We give the Krull-Stone representation theorem of fuzzy ideals in BL-algebras. Furthermore, we prove that the lattice of all fuzzy ideals of a BL-algebra is a complete distributive lattice. Finally, it is proved that every fuzzy Boolean ideal is a fuzzy Gödel ideal, but the converse implication is not true. PMID:24892085

  14. Teaching Machines to Think Fuzzy

    ERIC Educational Resources Information Center

    Technology Teacher, 2004

    2004-01-01

    Fuzzy logic programs for computers make them more human. Computers can then think through messy situations and make smart decisions. It makes computers able to control things the way people do. Fuzzy logic has been used to control subway trains, elevators, washing machines, microwave ovens, and cars. Pretty much all the human has to do is push one…

  15. Fuzzy models for pattern recognition

    SciTech Connect

    Bezdek, James C.; Pal, Sankar K.

    1994-01-01

    FUZZY sets were introduced in 1965 by Lotfi Zadeh as a new way to represent vagueness in everyday life. They are a generalization of conventional set theory, one of the basic structures underlying computational mathematics and models. Computational pattern recognition has played a central role in the development of fuzzy models because fuzzy interpretations of data structures are a very natural and intuitively plausible way to formulate and solve various problems. Fuzzy control theory has also provided a wide variety of real, fielded system applications of fuzzy technology. We shall have little more to say about the growth of fuzzy models in control, except to the extent that pattern recognition algorithms and methods described in this book impact control systems. Collected here are many of the seminal papers in the field. There will be, of course, omissions that are neither by intent nor ignorance; we cannot reproduce all of the important papers that have helped in the evolution of fuzzy pattern recognition (there may be as many as five hundred) even in this narrow application domain. We will attempt, in each chapter introduction, to comment on some of the important papers that not been included and we ask both readers and authors to understand that a book such as this simply cannot {open_quotes}contain everything.{close_quotes} Our objective in Chapter 1 is to describe the basic structure of fuzzy sets theory as it applies to the major problems encountered in the design of a pattern recognition system.

  16. Sequence analysis of Vicia faba repeated DNA, the FokI repeat element.

    PubMed Central

    Kato, A; Yakura, K; Tanifuji, S

    1984-01-01

    A type of highly repeated DNA sequences present in the genome of Vicia faba was detected by digestion its nuclear DNA with FokI endonuclease and fractionating the digests on polyacrylamide gels. Four fragments of 59, 108, 177 and 246 bp of the FokI repeated sequences were collected from the gels and their primary structures were determined by the method of Maxam and Gilbert. These repeated DNA sequences were shown to be a multiple tandem array of a 59 bp sequence element. And its nucleotide sequence was almost completely conserved among all the sequence members of each the size class and also among these classes. This sequence element consists of a duplet of an about the duplet has an incomplete dyad symmetrical structure. Images PMID:6089113

  17. Generalized interval-valued fuzzy variable precision rough sets determined by fuzzy logical operators

    NASA Astrophysics Data System (ADS)

    Qing Hu, Bao

    2015-11-01

    The fuzzy rough set model and interval-valued fuzzy rough set model have been introduced to handle databases with real values and interval values, respectively. Variable precision rough set was advanced by Ziarko to overcome the shortcomings of misclassification and/or perturbation in Pawlak rough sets. By combining fuzzy rough set and variable precision rough set, a variety of fuzzy variable precision rough sets were studied, which cannot only handle numerical data, but are also less sensitive to misclassification. However, fuzzy variable precision rough sets cannot effectively handle interval-valued data-sets. Research into interval-valued fuzzy rough sets for interval-valued fuzzy data-sets has commenced; however, variable precision problems have not been considered in interval-valued fuzzy rough sets and generalized interval-valued fuzzy rough sets based on fuzzy logical operators nor have interval-valued fuzzy sets been considered in variable precision rough sets and fuzzy variable precision rough sets. These current models are incapable of wide application, especially on misclassification and/or perturbation and on interval-valued fuzzy data-sets. In this paper, these models are generalized to a more integrative approach that not only considers interval-valued fuzzy sets, but also variable precision. First, we review generalized interval-valued fuzzy rough sets based on two fuzzy logical operators: interval-valued fuzzy triangular norms and interval-valued fuzzy residual implicators. Second, we propose generalized interval-valued fuzzy variable precision rough sets based on the above two fuzzy logical operators. Finally, we confirm that some existing models, including rough sets, fuzzy variable precision rough sets, interval-valued fuzzy rough sets, generalized fuzzy rough sets and generalized interval-valued fuzzy variable precision rough sets based on fuzzy logical operators, are special cases of the proposed models.

  18. Fuzzy θ-generalized semi-continuous and fuzzy θ-generalized semi-irresolute mappings

    NASA Astrophysics Data System (ADS)

    Wahab, Nurul Adilla Farhana Abdul; Salleh, Zabidin

    2015-10-01

    In this paper, some fuzzy generalized continuity are introduced and studied using the concept of fuzzy θ-generalized semi-closed sets namely fuzzy θ-generalized semi-continuity, fuzzy θ-generalized semi-irresolute and fuzzy θ-generalized semi-closed maps. Fuzzy θ-generalized semi-T1/2 spaces are also introduced and their characterizations are studied. Several interesting results are obtained.

  19. Fuzzy portfolio model with fuzzy-input return rates and fuzzy-output proportions

    NASA Astrophysics Data System (ADS)

    Tsaur, Ruey-Chyn

    2015-02-01

    In the finance market, a short-term investment strategy is usually applied in portfolio selection in order to reduce investment risk; however, the economy is uncertain and the investment period is short. Further, an investor has incomplete information for selecting a portfolio with crisp proportions for each chosen security. In this paper we present a new method of constructing fuzzy portfolio model for the parameters of fuzzy-input return rates and fuzzy-output proportions, based on possibilistic mean-standard deviation models. Furthermore, we consider both excess or shortage of investment in different economic periods by using fuzzy constraint for the sum of the fuzzy proportions, and we also refer to risks of securities investment and vagueness of incomplete information during the period of depression economics for the portfolio selection. Finally, we present a numerical example of a portfolio selection problem to illustrate the proposed model and a sensitivity analysis is realised based on the results.

  20. Fueling of tandem mirror reactors

    SciTech Connect

    Gorker, G.E.; Logan, B.G.

    1985-01-01

    This paper summarizes the fueling requirements for experimental and demonstration tandem mirror reactors (TMRs), reviews the status of conventional pellet injectors, and identifies some candidate accelerators that may be needed for fueling tandem mirror reactors. Characteristics and limitations of three types of accelerators are described; neutral beam injectors, electromagnetic rail guns, and laser beam drivers. Based on these characteristics and limitations, a computer module was developed for the Tandem Mirror Reactor Systems Code (TMRSC) to select the pellet injector/accelerator combination which most nearly satisfies the fueling requirements for a given machine design.

  1. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 3 2014-10-01 2014-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching...

  2. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching...

  3. Fuzzy conceptual rainfall runoff models

    NASA Astrophysics Data System (ADS)

    Özelkan, Ertunga C.; Duckstein, Lucien

    2001-11-01

    A fuzzy conceptual rainfall-runoff (CRR) framework is proposed herein to deal with those parameter uncertainties of conceptual rainfall-runoff models, that are related to data and/or model structure: with every element of the rainfall-runoff model assumed to be possibly uncertain, taken here as being fuzzy. First, the conceptual rainfall-runoff system is fuzzified and then different operational modes are formulated using fuzzy rules; second, the parameter identification aspect is examined using fuzzy regression techniques. In particular, bi-objective and tri-objective fuzzy regression models are applied in the case of linear conceptual rainfall-runoff models so that the decision maker may be able to trade off prediction vagueness (uncertainty) and the embedding outliers. For the non-linear models, a fuzzy least squares regression framework is applied to derive the model parameters. The methodology is illustrated using: (1) a linear conceptual rainfall-runoff model; (2) an experimental two-parameter model; and (3) a simplified version of the Sacramento soil moisture accounting model of the US National Weather Services river forecast system (SAC-SMA) known as the six-parameter model. It is shown that the fuzzy logic framework enables the decision maker to gain insight about the model sensitivity and the uncertainty stemming from the elements of the CRR model.

  4. Fuzzy resource optimization for safeguards

    SciTech Connect

    Zardecki, A.; Markin, J.T.

    1991-01-01

    Authorization, enforcement, and verification -- three key functions of safeguards systems -- form the basis of a hierarchical description of the system risk. When formulated in terms of linguistic rather than numeric attributes, the risk can be computed through an algorithm based on the notion of fuzzy sets. Similarly, this formulation allows one to analyze the optimal resource allocation by maximizing the overall detection probability, regarded as a linguistic variable. After summarizing the necessary elements of the fuzzy sets theory, we outline the basic algorithm. This is followed by a sample computation of the fuzzy optimization. 10 refs., 1 tab.

  5. Entanglement entropy on fuzzy spaces

    SciTech Connect

    Dou, Djamel; Ydri, Badis

    2006-08-15

    We study the entanglement entropy of a scalar field in 2+1 spacetime where space is modeled by a fuzzy sphere and a fuzzy disc. In both models we evaluate numerically the resulting entropies and find that they are proportional to the number of boundary degrees of freedom. In the Moyal plane limit of the fuzzy disc the entanglement entropy per unite area (length) diverges if the ignored region is of infinite size. The divergence is (interpreted) of IR-UV mixing origin. In general we expect the entanglement entropy per unite area to be finite on a noncommutative space if the ignored region is of finite size.

  6. Fuzzy expert systems using CLIPS

    NASA Technical Reports Server (NTRS)

    Le, Thach C.

    1994-01-01

    This paper describes a CLIPS-based fuzzy expert system development environment called FCLIPS and illustrates its application to the simulated cart-pole balancing problem. FCLIPS is a straightforward extension of CLIPS without any alteration to the CLIPS internal structures. It makes use of the object-oriented and module features in CLIPS version 6.0 for the implementation of fuzzy logic concepts. Systems of varying degrees of mixed Boolean and fuzzy rules can be implemented in CLIPS. Design and implementation issues of FCLIPS will also be discussed.

  7. Normal forms of fuzzy middle and fuzzy contradictions.

    PubMed

    Turksen, I B; Kandel, A; Zhang, Y Q

    1999-01-01

    The expressions of "excluded middle" and "crisp contradiction" are reexamined starting with their original linguistic expressions which are first restated in propositional and then predicate forms. It is shown that, in order to generalize the truth tables and hence the normal forms, the membership assignments in predicate expressions must be separated from their truth qualification. In two-valued logic, there is no need to separate them from each other due to reductionist Aristotalean dichotomy. Whereas, in infinite (fuzzy) valued set and logic, the separation of membership assignments from their truth qualification forms the bases of a new reconstruction of the truth tables. The results obtained from these extended truth tables are reducible to their Boolean equivalents under the axioms of Boolean theory. Whereas, in fuzzy set and logic theory, we obtain a richer and more complex interpretations of the "fuzzy middle" and "fuzzy contradiction." PMID:18252295

  8. Fuzzy Thinking in Non-Fuzzy Situations: Understanding Students' Perspective.

    ERIC Educational Resources Information Center

    Zazkis, Rina

    1995-01-01

    In mathematics a true statement is always true, but some false statements are more false than others. Fuzzy logic provides a way of handling degrees of set membership and has implications for helping students appreciate logical thinking. (MKR)

  9. Evaluation of fuzzy inference systems using fuzzy least squares

    NASA Technical Reports Server (NTRS)

    Barone, Joseph M.

    1992-01-01

    Efforts to develop evaluation methods for fuzzy inference systems which are not based on crisp, quantitative data or processes (i.e., where the phenomenon the system is built to describe or control is inherently fuzzy) are just beginning. This paper suggests that the method of fuzzy least squares can be used to perform such evaluations. Regressing the desired outputs onto the inferred outputs can provide both global and local measures of success. The global measures have some value in an absolute sense, but they are particularly useful when competing solutions (e.g., different numbers of rules, different fuzzy input partitions) are being compared. The local measure described here can be used to identify specific areas of poor fit where special measures (e.g., the use of emphatic or suppressive rules) can be applied. Several examples are discussed which illustrate the applicability of the method as an evaluation tool.

  10. Fuzzy Content-Based Retrieval in Image Databases.

    ERIC Educational Resources Information Center

    Wu, Jian Kang; Narasimhalu, A. Desai

    1998-01-01

    Proposes a fuzzy-image database model and a concept of fuzzy space; describes fuzzy-query processing in fuzzy space and fuzzy indexing on complete fuzzy vectors; and uses an example image database, the computer-aided facial-image inference and retrieval system (CAFIIR), for explanation throughout. (Author/LRW)

  11. A Fuzzy Query Mechanism for Human Resource Websites

    NASA Astrophysics Data System (ADS)

    Lai, Lien-Fu; Wu, Chao-Chin; Huang, Liang-Tsung; Kuo, Jung-Chih

    Users' preferences often contain imprecision and uncertainty that are difficult for traditional human resource websites to deal with. In this paper, we apply the fuzzy logic theory to develop a fuzzy query mechanism for human resource websites. First, a storing mechanism is proposed to store fuzzy data into conventional database management systems without modifying DBMS models. Second, a fuzzy query language is proposed for users to make fuzzy queries on fuzzy databases. User's fuzzy requirement can be expressed by a fuzzy query which consists of a set of fuzzy conditions. Third, each fuzzy condition associates with a fuzzy importance to differentiate between fuzzy conditions according to their degrees of importance. Fourth, the fuzzy weighted average is utilized to aggregate all fuzzy conditions based on their degrees of importance and degrees of matching. Through the mutual compensation of all fuzzy conditions, the ordering of query results can be obtained according to user's preference.

  12. Fuzzy logic components for iterative deconvolution systems

    NASA Astrophysics Data System (ADS)

    Northan, Brian M.

    2013-02-01

    Deconvolution systems rely heavily on expert knowledge and would benefit from approaches that capture this expert knowledge. Fuzzy logic is an approach that is used to capture expert knowledge rules and produce outputs that range in degree. This paper describes a fuzzy-deconvolution-system that integrates traditional Richardson-Lucy deconvolution with fuzzy components. The system is intended for restoration of 3D widefield images taken under conditions of refractive index mismatch. The system uses a fuzzy rule set for calculating sample refractive index, a fuzzy median filter for inter-iteration noise reduction, and a fuzzy rule set for stopping criteria.

  13. Knowledge representation in fuzzy logic

    NASA Technical Reports Server (NTRS)

    Zadeh, Lotfi A.

    1989-01-01

    The author presents a summary of the basic concepts and techniques underlying the application of fuzzy logic to knowledge representation. He then describes a number of examples relating to its use as a computational system for dealing with uncertainty and imprecision in the context of knowledge, meaning, and inference. It is noted that one of the basic aims of fuzzy logic is to provide a computational framework for knowledge representation and inference in an environment of uncertainty and imprecision. In such environments, fuzzy logic is effective when the solutions need not be precise and/or it is acceptable for a conclusion to have a dispositional rather than categorical validity. The importance of fuzzy logic derives from the fact that there are many real-world applications which fit these conditions, especially in the realm of knowledge-based systems for decision-making and control.

  14. Dynamical tachyons on fuzzy spheres

    SciTech Connect

    Berenstein, David; Trancanelli, Diego

    2011-05-15

    We study the spectrum of off-diagonal fluctuations between displaced fuzzy spheres in the Berenstein-Maldacena-Nastase plane wave matrix model. The displacement is along the plane of the fuzzy spheres. We find that when two fuzzy spheres intersect at angles, classical tachyons develop and that the spectrum of these modes can be computed analytically. These tachyons can be related to the familiar Nielsen-Olesen instabilities in Yang-Mills theory on a constant magnetic background. Many features of the problem become more apparent when we compare with maximally supersymmetric Yang-Mills theory on a sphere, of which this system is a truncation. We also set up a simple oscillatory trajectory on the displacement between the fuzzy spheres and study the dynamics of the modes as they become tachyonic for part of the oscillations. We speculate on their role regarding the possible thermalization of the system.

  15. Current projects in Fuzzy Control

    NASA Technical Reports Server (NTRS)

    Sugeno, Michio

    1990-01-01

    Viewgraphs on current projects in fuzzy control are presented. Three projects on helicopter flight control are discussed. The projects are (1) radio control by oral instructions; (2) automatic autorotation entry in engine failure; and (3) unmanned helicopter for sea rescue.

  16. Dynamical tachyons on fuzzy spheres

    NASA Astrophysics Data System (ADS)

    Berenstein, David; Trancanelli, Diego

    2011-05-01

    We study the spectrum of off-diagonal fluctuations between displaced fuzzy spheres in the Berenstein-Maldacena-Nastase plane wave matrix model. The displacement is along the plane of the fuzzy spheres. We find that when two fuzzy spheres intersect at angles, classical tachyons develop and that the spectrum of these modes can be computed analytically. These tachyons can be related to the familiar Nielsen-Olesen instabilities in Yang-Mills theory on a constant magnetic background. Many features of the problem become more apparent when we compare with maximally supersymmetric Yang-Mills theory on a sphere, of which this system is a truncation. We also set up a simple oscillatory trajectory on the displacement between the fuzzy spheres and study the dynamics of the modes as they become tachyonic for part of the oscillations. We speculate on their role regarding the possible thermalization of the system.

  17. Telomeric Repeat Mutagenicity in Human Somatic Cells is Modulated by Repeat Orientation and G-Quadruplex Stability

    PubMed Central

    Damerla, Rama Rao; Knickelbein, Kelly E.; Kepchia, Devin; Jackson, Abbe; Armitage, Bruce A.; Eckert, Kristin A.; Opresko, Patricia L.

    2010-01-01

    Telomeres consisting of tandem guanine-rich repeats can form secondary DNA structures called G-quadruplexes that represent potential targets for DNA repair enzymes. While G-quadruplexes interfere with DNA synthesis in vitro, the impact of G-quadruplex formation on telomeric repeat replication in human cells is not clear. We investigated the mutagenicity of telomeric repeats as a function of G-quadruplex folding opportunity and thermal stability using a shuttle vector mutagenesis assay. Since single stranded DNA during lagging strand replication increases the opportunity for G-quadruplex folding, we tested vectors with G-rich sequences on the lagging versus the leading strand. Contrary to our prediction, vectors containing human [TTAGGG]10 repeats with a G-rich lagging strand were significantly less mutagenic than vectors with a G-rich leading strand, after replication in normal human cells. We show by UV melting experiments that G-quadruplexes from ciliates [TTGGGG]4 and [TTTTGGGG]4 are thermally more stable compared to human [TTAGGG]4. Consistent with this, replication of vectors with ciliate [TTGGGG]10 repeats yielded a 3-fold higher mutant rate compared to the human [TTAGGG]10 vectors. Furthermore, we observed significantly more mutagenic events in the ciliate repeats compared to the human repeats. Our data demonstrate that increased G-quadruplex opportunity (repeat orientation) in human telomeric repeats decreased mutagenicity, while increased thermal stability of telomeric G-qaudruplexes was associated with increased mutagenicity. PMID:20800555

  18. Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats.

    PubMed

    Dao, Thuy P; Majumdar, Ananya; Barrick, Doug

    2014-06-01

    Capping motifs are found to flank most β-strand-containing repeat proteins. To better understand the roles of these capping motifs in organizing structure and stability, we carried out folding and solution NMR studies on the leucine-rich repeat (LRR) domain of PP32, which is composed of five tandem LRR, capped by α-helical and β-hairpin motifs on the N- and C-termini. We were able to purify PP32 constructs lacking either cap and containing destabilizing substitutions. Removing the C-cap results in complete unfolding of PP32. Removing the N-cap has a much less severe effect, decreasing stability but retaining much of its secondary structure. In contrast, the dynamics and tertiary structure of the first two repeats are significantly perturbed, based on (1)H-(15)N relaxation studies, chemical shift perturbations, and residual dipolar couplings. However, more distal repeats (3 to C-cap) retain their native tertiary structure. In this regard, the N-cap drives the folding of adjacent repeats from what appears to be a molten-globule-like state. This interpretation is supported by extensive analysis using core packing substitutions in the full-length and N-cap-truncated PP32. This work highlights the importance of caps to the stability and structural integrity of β-strand-containing LRR proteins, and emphasizes the different contributions of the N- and C-terminal caps. PMID:24659532

  19. Fuzzy Logic Particle Tracking

    NASA Technical Reports Server (NTRS)

    2005-01-01

    A new all-electronic Particle Image Velocimetry technique that can efficiently map high speed gas flows has been developed in-house at the NASA Lewis Research Center. Particle Image Velocimetry is an optical technique for measuring the instantaneous two component velocity field across a planar region of a seeded flow field. A pulsed laser light sheet is used to illuminate the seed particles entrained in the flow field at two instances in time. One or more charged coupled device (CCD) cameras can be used to record the instantaneous positions of particles. Using the time between light sheet pulses and determining either the individual particle displacements or the average displacement of particles over a small subregion of the recorded image enables the calculation of the fluid velocity. Fuzzy logic minimizes the required operator intervention in identifying particles and computing velocity. Using two cameras that have the same view of the illumination plane yields two single exposure image frames. Two competing techniques that yield unambiguous velocity vector direction information have been widely used for reducing the single-exposure, multiple image frame data: (1) cross-correlation and (2) particle tracking. Correlation techniques yield averaged velocity estimates over subregions of the flow, whereas particle tracking techniques give individual particle velocity estimates. For the correlation technique, the correlation peak corresponding to the average displacement of particles across the subregion must be identified. Noise on the images and particle dropout result in misidentification of the true correlation peak. The subsequent velocity vector maps contain spurious vectors where the displacement peaks have been improperly identified. Typically these spurious vectors are replaced by a weighted average of the neighboring vectors, thereby decreasing the independence of the measurements. In this work, fuzzy logic techniques are used to determine the true

  20. Reconfigurable multiport EPON repeater

    NASA Astrophysics Data System (ADS)

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio

    2009-11-01

    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  1. A Novel Method for Discovering Fuzzy Sequential Patterns Using the Simple Fuzzy Partition Method.

    ERIC Educational Resources Information Center

    Chen, Ruey-Shun; Hu, Yi-Chung

    2003-01-01

    Discusses sequential patterns, data mining, knowledge acquisition, and fuzzy sequential patterns described by natural language. Proposes a fuzzy data mining technique to discover fuzzy sequential patterns by using the simple partition method which allows the linguistic interpretation of each fuzzy set to be easily obtained. (Author/LRW)

  2. Tandem Cylinder Noise Predictions

    NASA Technical Reports Server (NTRS)

    Lockhard, David P.; Khorrami, Mehdi R.; CHoudhari, Meelan M.; Hutcheson, Florence V.; Brooks, Thomas F.; Stead, Daniel J.

    2007-01-01

    In an effort to better understand landing-gear noise sources, we have been examining a simplified configuration that still maintains some of the salient features of landing-gear flow fields. In particular, tandem cylinders have been studied because they model a variety of component level interactions. The present effort is directed at the case of two identical cylinders spatially separated in the streamwise direction by 3.7 diameters. Experimental measurements from the Basic Aerodynamic Research Tunnel (BART) and Quiet Flow Facility (QFF) at NASA Langley Research Center (LaRC) have provided steady surface pressures, detailed off-surface measurements of the flow field using Particle Image Velocimetry (PIV), hot-wire measurements in the wake of the rear cylinder, unsteady surface pressure data, and the radiated noise. The experiments were conducted at a Reynolds number of 166 105 based on the cylinder diameter. A trip was used on the upstream cylinder to insure a fully turbulent shedding process and simulate the effects of a high Reynolds number flow. The parallel computational effort uses the three-dimensional Navier-Stokes solver CFL3D with a hybrid, zonal turbulence model that turns off the turbulence production term everywhere except in a narrow ring surrounding solid surfaces. The current calculations further explore the influence of the grid resolution and spanwise extent on the flow and associated radiated noise. Extensive comparisons with the experimental data are used to assess the ability of the computations to simulate the details of the flow. The results show that the pressure fluctuations on the upstream cylinder, caused by vortex shedding, are smaller than those generated on the downstream cylinder by wake interaction. Consequently, the downstream cylinder dominates the noise radiation, producing an overall directivity pattern that is similar to that of an isolated cylinder. Only calculations based on the full length of the model span were able to

  3. Quantum repeated games revisited

    NASA Astrophysics Data System (ADS)

    Frąckiewicz, Piotr

    2012-03-01

    We present a scheme for playing quantum repeated 2 × 2 games based on Marinatto and Weber’s approach to quantum games. As a potential application, we study the twice repeated Prisoner’s Dilemma game. We show that results not available in the classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games proposed by Iqbal and Toor. We point out the drawbacks that make their results unacceptable.

  4. Lorentzian fuzzy spheres

    NASA Astrophysics Data System (ADS)

    Chaney, A.; Lu, Lei; Stern, A.

    2015-09-01

    We show that fuzzy spheres are solutions of Lorentzian Ishibashi-Kawai-Kitazawa-Tsuchiya-type matrix models. The solutions serve as toy models of closed noncommutative cosmologies where big bang/crunch singularities appear only after taking the commutative limit. The commutative limit of these solutions corresponds to a sphere embedded in Minkowski space. This "sphere" has several novel features. The induced metric does not agree with the standard metric on the sphere, and, moreover, it does not have a fixed signature. The curvature computed from the induced metric is not constant, has singularities at fixed latitudes (not corresponding to the poles) and is negative. Perturbations are made about the solutions, and are shown to yield a scalar field theory on the sphere in the commutative limit. The scalar field can become tachyonic for a range of the parameters of the theory.

  5. Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array.

    PubMed

    Mendez, Gregory S; Delwiche, Charles F; Apt, Kirk E; Lippmeier, J Casey

    2015-01-01

    Dinoflagellates are one of the last major lineages of eukaryotes for which little is known about genome structure and organization. We report here the sequence and gene structure of a clone isolated from a cosmid library which, to our knowledge, represents the largest contiguously sequenced, dinoflagellate genomic, tandem gene array. These data, combined with information from a large transcriptomic library, allowed a high level of confidence of every base pair call. This degree of confidence is not possible with PCR-based contigs. The sequence contains an intron-rich set of five highly expressed gene repeats arranged in tandem. One of the tandem repeat gene members contains an intron 26,372 bp long. This study characterizes a splice site consensus sequence for dinoflagellate introns. Two to nine base pairs around the 3' splice site are repeated by an identical two to nine base pairs around the 5' splice site. The 5' and 3' splice sites are in the same locations within each repeat so that the repeat is found only once in the mature mRNA. This identically repeated intron boundary sequence might be useful in gene modeling and annotation of genomes. PMID:25963315

  6. Fuzzy tuning B-spline curve

    NASA Astrophysics Data System (ADS)

    Fatah, Abd.; Rozaimi

    2015-12-01

    In this paper, we will discuss about the construction of fuzzy tuning B-spline curve based on fuzzy set theory. The concept of fuzzy tuning in designing this B-spline curve is based on the uncertain knots values which has to be defined first and then the result will be blended together with B-spline function which exists in users presumption in deciding the best knots value of tuning. Therefore, fuzzy set theory especially fuzzy number concepts are used to define the uncertain knots values and then it will be become fuzzy knots values. The Result by using different values of fuzzy knots for constructing a fuzzy tuning of B-spline curves will be illustrated.

  7. The Lattices of Group Fuzzy Congruences and Normal Fuzzy Subsemigroups on E-Inversive Semigroups

    PubMed Central

    Wang, Shoufeng

    2014-01-01

    The aim of this paper is to investigate the lattices of group fuzzy congruences and normal fuzzy subsemigroups on E-inversive semigroups. We prove that group fuzzy congruences and normal fuzzy subsemigroups determined each other in E-inversive semigroups. Moreover, we show that the set of group t-fuzzy congruences and the set of normal subsemigroups with tip t in a given E-inversive semigroup form two mutually isomorphic modular lattices for every t∈ [0,1]. PMID:24892045

  8. Consistent linguistic fuzzy preference relations method with ranking fuzzy numbers

    NASA Astrophysics Data System (ADS)

    Ridzuan, Siti Amnah Mohd; Mohamad, Daud; Kamis, Nor Hanimah

    2014-12-01

    Multi-Criteria Decision Making (MCDM) methods have been developed to help decision makers in selecting the best criteria or alternatives from the options given. One of the well known methods in MCDM is the Consistent Fuzzy Preference Relation (CFPR) method, essentially utilizes a pairwise comparison approach. This method was later improved to cater subjectivity in the data by using fuzzy set, known as the Consistent Linguistic Fuzzy Preference Relations (CLFPR). The CLFPR method uses the additive transitivity property in the evaluation of pairwise comparison matrices. However, the calculation involved is lengthy and cumbersome. To overcome this problem, a method of defuzzification was introduced by researchers. Nevertheless, the defuzzification process has a major setback where some information may lose due to the simplification process. In this paper, we propose a method of CLFPR that preserves the fuzzy numbers form throughout the process. In obtaining the desired ordering result, a method of ranking fuzzy numbers is utilized in the procedure. This improved procedure for CLFPR is implemented to a case study to verify its effectiveness. This method is useful for solving decision making problems and can be applied to many areas of applications.

  9. Fuzzy logic and neural networks

    SciTech Connect

    Loos, J.R.

    1994-11-01

    Combine fuzzy logic`s fuzzy sets, fuzzy operators, fuzzy inference, and fuzzy rules - like defuzzification - with neural networks and you can arrive at very unfuzzy real-time control. Fuzzy logic, cursed with a very whimsical title, simply means multivalued logic, which includes not only the conventional two-valued (true/false) crisp logic, but also the logic of three or more values. This means one can assign logic values of true, false, and somewhere in between. This is where fuzziness comes in. Multi-valued logic avoids the black-and-white, all-or-nothing assignment of true or false to an assertion. Instead, it permits the assignment of shades of gray. When assigning a value of true or false to an assertion, the numbers typically used are {open_quotes}1{close_quotes} or {open_quotes}0{close_quotes}. This is the case for programmed systems. If {open_quotes}0{close_quotes} means {open_quotes}false{close_quotes} and {open_quotes}1{close_quotes} means {open_quotes}true,{close_quotes} then {open_quotes}shades of gray{close_quotes} are any numbers between 0 and 1. Therefore, {open_quotes}nearly true{close_quotes} may be represented by 0.8 or 0.9, {open_quotes}nearly false{close_quotes} may be represented by 0.1 or 0.2, and {close_quotes}your guess is as good as mine{close_quotes} may be represented by 0.5. The flexibility available to one is limitless. One can associate any meaning, such as {open_quotes}nearly true{close_quotes}, to any value of any granularity, such as 0.9999. 2 figs.

  10. Fuzzy image processing in sun sensor

    NASA Technical Reports Server (NTRS)

    Mobasser, S.; Liebe, C. C.; Howard, A.

    2003-01-01

    This paper will describe how the fuzzy image processing is implemented in the instrument. Comparison of the Fuzzy image processing and a more conventional image processing algorithm is provided and shows that the Fuzzy image processing yields better accuracy then conventional image processing.

  11. Forecasting Enrollments with Fuzzy Time Series.

    ERIC Educational Resources Information Center

    Song, Qiang; Chissom, Brad S.

    The concept of fuzzy time series is introduced and used to forecast the enrollment of a university. Fuzzy time series, an aspect of fuzzy set theory, forecasts enrollment using a first-order time-invariant model. To evaluate the model, the conventional linear regression technique is applied and the predicted values obtained are compared to the…

  12. Fuzzy-algebra uncertainty assessment

    SciTech Connect

    Cooper, J.A.; Cooper, D.K.

    1994-12-01

    A significant number of analytical problems (for example, abnormal-environment safety analysis) depend on data that are partly or mostly subjective. Since fuzzy algebra depends on subjective operands, we have been investigating its applicability to these forms of assessment, particularly for portraying uncertainty in the results of PRA (probabilistic risk analysis) and in risk-analysis-aided decision-making. Since analysis results can be a major contributor to a safety-measure decision process, risk management depends on relating uncertainty to only known (not assumed) information. The uncertainties due to abnormal environments are even more challenging than those in normal-environment safety assessments; and therefore require an even more judicious approach. Fuzzy algebra matches these requirements well. One of the most useful aspects of this work is that we have shown the potential for significant differences (especially in perceived margin relative to a decision threshold) between fuzzy assessment and probabilistic assessment based on subtle factors inherent in the choice of probability distribution models. We have also shown the relation of fuzzy algebra assessment to ``bounds`` analysis, as well as a description of how analyses can migrate from bounds analysis to fuzzy-algebra analysis, and to probabilistic analysis as information about the process to be analyzed is obtained. Instructive examples are used to illustrate the points.

  13. Imprecise (fuzzy) information in geostatistics

    SciTech Connect

    Bardossy, A.; Bogardi, I.; Kelly, W.E.

    1988-05-01

    A methodology based on fuzzy set theory for the utilization of imprecise data in geostatistics is presented. A common problem preventing a broader use of geostatistics has been the insufficient amount of accurate measurement data. In certain cases, additional but uncertain (soft) information is available and can be encoded as subjective probabilities, and then the soft kriging method can be applied (Journal, 1986). In other cases, a fuzzy encoding of soft information may be more realistic and simplify the numerical calculations. Imprecise (fuzzy) spatial information on the possible variogram is integrated into a single variogram which is used in a fuzzy kriging procedure. The overall uncertainty of prediction is represented by the estimation variance and the calculated membership function for each kriged point. The methodology is applied to the permeability prediction of a soil liner for hazardous waste containment. The available number of hard measurement data (20) was not enough for a classical geostatistical analysis. An additional 20 soft data made it possible to prepare kriged contour maps using the fuzzy geostatistical procedure.

  14. Fuzzy logic of Aristotelian forms

    SciTech Connect

    Perlovsky, L.I.

    1996-12-31

    Model-based approaches to pattern recognition and machine vision have been proposed to overcome the exorbitant training requirements of earlier computational paradigms. However, uncertainties in data were found to lead to a combinatorial explosion of the computational complexity. This issue is related here to the roles of a priori knowledge vs. adaptive learning. What is the a-priori knowledge representation that supports learning? I introduce Modeling Field Theory (MFT), a model-based neural network whose adaptive learning is based on a priori models. These models combine deterministic, fuzzy, and statistical aspects to account for a priori knowledge, its fuzzy nature, and data uncertainties. In the process of learning, a priori fuzzy concepts converge to crisp or probabilistic concepts. The MFT is a convergent dynamical system of only linear computational complexity. Fuzzy logic turns out to be essential for reducing the combinatorial complexity to linear one. I will discuss the relationship of the new computational paradigm to two theories due to Aristotle: theory of Forms and logic. While theory of Forms argued that the mind cannot be based on ready-made a priori concepts, Aristotelian logic operated with just such concepts. I discuss an interpretation of MFT suggesting that its fuzzy logic, combining a-priority and adaptivity, implements Aristotelian theory of Forms (theory of mind). Thus, 2300 years after Aristotle, a logic is developed suitable for his theory of mind.

  15. Construction of fuzzy S{sup 4}

    SciTech Connect

    Abe, Yasuhiro

    2004-12-15

    We construct a fuzzy S{sup 4}, utilizing the fact that CP{sup 3} is an S{sup 2} bundle over S{sup 4}. We find that the fuzzy S{sup 4} can be described by a block-diagonal form whose embedding square matrix represents a fuzzy CP{sup 3}. We discuss some pending issues on fuzzy S{sup 4}, i.e., precise matrix-function correspondence, associativity of the algebra, and, etc. Similarly, we also obtain a fuzzy S{sup 8}, using the fact that CP{sup 7} is a CP{sup 3} bundle over S{sup 8}.

  16. Parallel Fuzzy Segmentation of Multiple Objects.

    PubMed

    Garduño, Edgar; Herman, Gabor T

    2008-01-01

    The usefulness of fuzzy segmentation algorithms based on fuzzy connectedness principles has been established in numerous publications. New technologies are capable of producing larger-and-larger datasets and this causes the sequential implementations of fuzzy segmentation algorithms to be time-consuming. We have adapted a sequential fuzzy segmentation algorithm to multi-processor machines. We demonstrate the efficacy of such a distributed fuzzy segmentation algorithm by testing it with large datasets (of the order of 50 million points/voxels/items): a speed-up factor of approximately five over the sequential implementation seems to be the norm. PMID:19444333

  17. Effect of noise on chaotic fuzzy mappings

    SciTech Connect

    Zardecki, A.

    1996-03-01

    Chaotic mappings in the space of fuzzy sets induced by mappings of the underlying reference set are investigated. Different fuzzification schemes are considered and their impact on the resultant iterated fuzzy set, under a quadratic mapping, is studied numerically. The fuzzy set mapping is described in terms of the mapping of level cuts, resulting from the resolution theorem for fuzzy sets. In the two-dimensional case, a generalized notion, given as a fuzzy set, of the Hausdorff dimension is formulated. An example, based on the Henon Mapping, is provided.

  18. Fuzzy reliability analysis of structures by using the method of fuzzy optimization

    SciTech Connect

    Hu, Y.; Chen, B.

    1996-12-31

    There are two kinds of uncertainties in safety assessment of engineering structures. One is of the nature of randomness, and the other fuzziness. Fuzzy uncertainties exist in defining certain structural performances, conditions, parameters, and their interrelationships. The theory of fuzzy sets should be employed to cope with the fuzzy uncertainties. In this paper, a general definition for structural failure considering the fuzzy uncertainties is introduced firstly. Failure of the structure is modelled by a fuzzy event, and described by the membership function. The limit state surface is then replaced by a fuzzy limit state zone, in which every point represents a state belonging to the failure with a certain degree of membership. Then a fuzzy optimization problem for solving the reliability index is formulated. In classical structural reliability theory, the reliability index is defined by the minimum distance from the limit state surface to the origin of the standard normal variable space. It can be evaluated by solving an optimization problem. When the fuzzy uncertainties are taken into consideration, the crisp limit state surface becomes a fuzzy limit state zone. In this case, a corresponding fuzzy optimization problem can be formulated. Fuzzy reliability index can be obtained by solving the fuzzy optimization problem by an iterative procedure with some criteria base on the fuzzy decision-making. Numerical examples are given in the paper.

  19. Fuzzy sensitivity analysis for reliability assessment of building structures

    NASA Astrophysics Data System (ADS)

    Kala, Zdeněk

    2016-06-01

    The mathematical concept of fuzzy sensitivity analysis, which studies the effects of the fuzziness of input fuzzy numbers on the fuzziness of the output fuzzy number, is described in the article. The output fuzzy number is evaluated using Zadeh's general extension principle. The contribution of stochastic and fuzzy uncertainty in reliability analysis tasks of building structures is discussed. The algorithm of fuzzy sensitivity analysis is an alternative to stochastic sensitivity analysis in tasks in which input and output variables are considered as fuzzy numbers.

  20. Discovering fuzzy spatial association rules

    NASA Astrophysics Data System (ADS)

    Kacar, Esen; Cicekli, Nihan K.

    2002-03-01

    Discovering interesting, implicit knowledge and general relationships in geographic information databases is very important to understand and use these spatial data. One of the methods for discovering this implicit knowledge is mining spatial association rules. A spatial association rule is a rule indicating certain association relationships among a set of spatial and possibly non-spatial predicates. In the mining process, data is organized in a hierarchical manner. However, in real-world applications it may not be possible to construct a crisp structure for this data, instead some fuzzy structures should be used. Fuzziness, i.e. partial belonging of an item to more than one sub-item in the hierarchy, could be applied to the data itself, and also to the hierarchy of spatial relations. This paper shows that, strong association rules can be mined from large spatial databases using fuzzy concept and spatial relation hierarchies.

  1. Honesty through repeated interactions.

    PubMed

    Rich, Patricia; Zollman, Kevin J S

    2016-04-21

    In the study of signaling, it is well known that the cost of deception is an essential element for stable honest signaling in nature. In this paper, we show how costs for deception can arise endogenously from repeated interactions between individuals. Utilizing the Sir Philip Sidney game as an illustrative case, we show that repeated interactions can sustain honesty with no observable signal costs, even when deception cannot be directly observed. We provide a number of potential experimental tests for this theory which distinguish it from the available alternatives. PMID:26869213

  2. Fuzzy lattice neurocomputing (FLN) models.

    PubMed

    Kaburlasos, V G; Petridis, V

    2000-12-01

    In this work it is shown how fuzzy lattice neurocomputing (FLN) emerges as a connectionist paradigm in the framework of fuzzy lattices (FL-framework) whose advantages include the capacity to deal rigorously with: disparate types of data such as numeric and linguistic data, intervals of values, 'missing' and 'don't care' data. A novel notation for the FL-framework is introduced here in order to simplify mathematical expressions without losing content. Two concrete FLN models are presented, namely 'sigma-FLN' for competitive clustering, and 'FLN with tightest fits (FLNtf)' for supervised clustering. Learning by the sigma-FLN, is rapid as it requires a single pass through the data, whereas learning by the FLNtf, is incremental, data order independent, polynomial theta(n3), and it guarantees maximization of the degree of inclusion of an input in a learned class as explained in the text. Convenient geometric interpretations are provided. The sigma-FLN is presented here as fuzzy-ART's extension in the FL-framework such that sigma-FLN widens fuzzy-ART's domain of application to (mathematical) lattices by augmenting the scope of both of fuzzy-ART's choice (Weber) and match functions, and by enhancing fuzzy-ART's complement coding technique. The FLNtf neural model is applied to four benchmark data sets of various sizes for pattern recognition and rule extraction. The benchmark data sets in question involve jointly numeric and nominal data with 'missing' and/or 'don't care' attribute values, whereas the lattices involved include the unit-hypercube, a probability space, and a Boolean algebra. The potential of the FL-framework in computing is also delineated. PMID:11156192

  3. Learning and Tuning of Fuzzy Rules

    NASA Technical Reports Server (NTRS)

    Berenji, Hamid R.

    1997-01-01

    In this chapter, we review some of the current techniques for learning and tuning fuzzy rules. For clarity, we refer to the process of generating rules from data as the learning problem and distinguish it from tuning an already existing set of fuzzy rules. For learning, we touch on unsupervised learning techniques such as fuzzy c-means, fuzzy decision tree systems, fuzzy genetic algorithms, and linear fuzzy rules generation methods. For tuning, we discuss Jang's ANFIS architecture, Berenji-Khedkar's GARIC architecture and its extensions in GARIC-Q. We show that the hybrid techniques capable of learning and tuning fuzzy rules, such as CART-ANFIS, RNN-FLCS, and GARIC-RB, are desirable in development of a number of future intelligent systems.

  4. Expert systems and fuzzy systems

    SciTech Connect

    Negoita, C.

    1985-01-01

    This book examines the design of the expert computer system and how fuzzy systems can be used to deal with imprecise information. As the author explores the effects of semantic systems on decision support systems, he asserts that the utilization of fuzzy set theory can help an expert system draw from its knowledge base more efficiently and therefore make more accurate and reliable decisions. The book includes realistic status reports in approximate reasoning and knowledge representation that are supported by a ''theory of categories'' mathematical approach. The differences between symbolic and semantic manipulation are outline, and detailed information is given on the actual theory of knowledge-based systems.

  5. The semantics of fuzzy logic

    NASA Technical Reports Server (NTRS)

    Ruspini, Enrique H.

    1991-01-01

    Summarized here are the results of recent research on the conceptual foundations of fuzzy logic. The focus is primarily on the principle characteristics of a model that quantifies resemblance between possible worlds by means of a similarity function that assigns a number between 0 and 1 to every pair of possible worlds. Introduction of such a function permits one to interpret the major constructs and methods of fuzzy logic: conditional and unconditional possibility and necessity distributions and the generalized modus ponens of Zadeh on the basis of related metric relationships between subsets of possible worlds.

  6. Fuzzy simulation in concurrent engineering

    NASA Technical Reports Server (NTRS)

    Kraslawski, A.; Nystrom, L.

    1992-01-01

    Concurrent engineering is becoming a very important practice in manufacturing. A problem in concurrent engineering is the uncertainty associated with the values of the input variables and operating conditions. The problem discussed in this paper concerns the simulation of processes where the raw materials and the operational parameters possess fuzzy characteristics. The processing of fuzzy input information is performed by the vertex method and the commercial simulation packages POLYMATH and GEMS. The examples are presented to illustrate the usefulness of the method in the simulation of chemical engineering processes.

  7. Universal fuzzy models and universal fuzzy controllers for discrete-time nonlinear systems.

    PubMed

    Gao, Qing; Feng, Gang; Dong, Daoyi; Liu, Lu

    2015-05-01

    This paper investigates the problems of universal fuzzy model and universal fuzzy controller for discrete-time nonaffine nonlinear systems (NNSs). It is shown that a kind of generalized T-S fuzzy model is the universal fuzzy model for discrete-time NNSs satisfying a sufficient condition. The results on universal fuzzy controllers are presented for two classes of discrete-time stabilizable NNSs. Constructive procedures are provided to construct the model reference fuzzy controllers. The simulation example of an inverted pendulum is presented to illustrate the effectiveness and advantages of the proposed method. These results significantly extend the approach for potential applications in solving complex engineering problems. PMID:25137736

  8. Triggering of repeated earthquakes

    NASA Astrophysics Data System (ADS)

    Sobolev, G. A.; Zakrzhevskaya, N. A.; Sobolev, D. G.

    2016-03-01

    Based on the analysis of the world's earthquakes with magnitudes M ≥ 6.5 for 1960-2013, it is shown that they cause global-scale coherent seismic oscillations which most distinctly manifest themselves in the period interval of 4-6 min during 1-3 days after the event. After these earthquakes, a repeated shock has an increased probability to occur in different seismically active regions located as far away as a few thousand km from the previous event, i.e., a remote interaction of seismic events takes place. The number of the repeated shocks N( t) decreases with time, which characterizes the memory of the lithosphere about the impact that has occurred. The time decay N( t) can be approximated by the linear, exponential, and powerlaw dependences. No distinct correlation between the spatial locations of the initial and repeated earthquakes is revealed. The probable triggering mechanisms of the remote interaction between the earthquakes are discussed. Surface seismic waves traveling several times around the Earth's, coherent oscillations, and global source are the most preferable candidates. This may lead to the accumulation and coalescence of ruptures in the highly stressed or weakened domains of a seismically active region, which increases the probability of a repeated earthquake.

  9. Repeated Causal Decision Making

    ERIC Educational Resources Information Center

    Hagmayer, York; Meder, Bjorn

    2013-01-01

    Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in…

  10. Bidirectional Manchester repeater

    NASA Technical Reports Server (NTRS)

    Ferguson, J.

    1980-01-01

    Bidirectional Manchester repeater is inserted at periodic intervals along single bidirectional twisted pair transmission line to detect, amplify, and transmit bidirectional Manchester 11 code signals. Requiring only 18 TTL 7400 series IC's, some line receivers and drivers, and handful of passive components, circuit is simple and relatively inexpensive to build.

  11. A fuzzy control design case: The fuzzy PLL

    NASA Technical Reports Server (NTRS)

    Teodorescu, H. N.; Bogdan, I.

    1992-01-01

    The aim of this paper is to present a typical fuzzy control design case. The analyzed controlled systems are the phase-locked loops (PLL's)--classic systems realized in both analogic and digital technology. The crisp PLL devices are well known.

  12. Fuzzy set applications in engineering optimization: Multilevel fuzzy optimization

    NASA Technical Reports Server (NTRS)

    Diaz, Alejandro R.

    1989-01-01

    A formulation for multilevel optimization with fuzzy objective functions is presented. With few exceptions, formulations for fuzzy optimization have dealt with a one-level problem in which the objective is the membership function of a fuzzy set formed by the fuzzy intersection of other sets. In the problem examined here, the goal set G is defined in a more general way, using an aggregation operator H that allows arbitrary combinations of set operations (union, intersection, addition) on the individual sets Gi. This is a straightforward extension of the standard form, but one that makes possible the modeling of interesting evaluation strategies. A second, more important departure from the standard form will be the construction of a multilevel problem analogous to the design decomposition problem in optimization. This arrangement facilitates the simulation of a system design process in which different components of the system are designed by different teams, and different levels of design detail become relevant at different time stages in the process: global design features early, local features later in the process.

  13. The Repeat Region of the Circumsporozoite Protein is Critical for Sporozoite Formation and Maturation in Plasmodium

    PubMed Central

    Patzewitz, Eva-Maria; Wall, Richard J.; Hopp, Christine S.; Poulin, Benoit; Mohmmed, Asif; Malhotra, Pawan; Coppi, Alida; Sinnis, Photini; Tewari, Rita

    2014-01-01

    The circumsporozoite protein (CSP) is the major surface protein of the sporozoite stage of malaria parasites and has multiple functions as the parasite develops and then migrates from the mosquito midgut to the mammalian liver. The overall structure of CSP is conserved among Plasmodium species, consisting of a species-specific central tandem repeat region flanked by two conserved domains: the NH2-terminus and the thrombospondin repeat (TSR) at the COOH-terminus. Although the central repeat region is an immunodominant B-cell epitope and the basis of the only candidate malaria vaccine in Phase III clinical trials, little is known about its functional role(s). We used the rodent malaria model Plasmodium berghei to investigate the role of the CSP tandem repeat region during sporozoite development. Here we describe two mutant parasite lines, one lacking the tandem repeat region (ΔRep) and the other lacking the NH2-terminus as well as the repeat region (ΔNΔRep). We show that in both mutant lines oocyst formation is unaffected but sporozoite development is defective. PMID:25438048

  14. Fuzzy coordinator in control problems

    NASA Technical Reports Server (NTRS)

    Rueda, A.; Pedrycz, W.

    1992-01-01

    In this paper a hierarchical control structure using a fuzzy system for coordination of the control actions is studied. The architecture involves two levels of control: a coordination level and an execution level. Numerical experiments will be utilized to illustrate the behavior of the controller when it is applied to a nonlinear plant.

  15. Soft computing and fuzzy logic

    SciTech Connect

    Zadeh, L.A.

    1994-12-31

    Soft computing is a collection of methodologies that aim to exploit the tolerance for imprecision and uncertainty to achieve tractability, robustness, and low solution cost. Its principal constituents are fuzzy logic, neuro-computing, and probabilistic reasoning. Soft computing is likely to play an increasingly important role in many application areas, including software engineering. The role model for soft computing is the human mind.

  16. Fuzzy control system for a mobile robot

    SciTech Connect

    Hai Quan Dai; Dalton, G.R.; Tulenko, J. )

    1992-01-01

    Since the first fuzzy logic control system was proposed by Mamdani, many studies have been carried out on industrial process and real-time controls. The key problem for the application of fuzzy logic control is to find a suitable set of fuzzy control rules. Three common modes of deriving fuzzy control rules are often distinguished and mentioned: (1) expert experience and knowledge; (2) modeling operator control actions; and (3) modeling a process. In cases where an operator's skill is important, it is very useful to derive fuzzy control rules by modeling an operator's control actions. It is possible to model an operator's control behaviors in terms of fuzzy implications using the input-output data concerned with his/her control actions. The authors use the model obtained in this way as the basis for a fuzzy controller. The authors use a finite number of fuzzy or approximate control rules. To control a robot in a cluttered reactor environment, it is desirable to combine all the methods. In this paper, the authors describe a general algorithm for a mobile robot control system with fuzzy logic reasoning. They discuss the way that knowledge of fuzziness will be represented in this control system. They also describe a simulation program interface to the K2A Cybermation mobile robot to be used to demonstrate the control system.

  17. Fuzzy tree automata and syntactic pattern recognition.

    PubMed

    Lee, E T

    1982-04-01

    An approach of representing patterns by trees and processing these trees by fuzzy tree automata is described. Fuzzy tree automata are defined and investigated. The results include that the class of fuzzy root-to-frontier recognizable ¿-trees is closed under intersection, union, and complementation. Thus, the class of fuzzy root-to-frontier recognizable ¿-trees forms a Boolean algebra. Fuzzy tree automata are applied to processing fuzzy tree representation of patterns based on syntactic pattern recognition. The grade of acceptance is defined and investigated. Quantitative measures of ``approximate isosceles triangle,'' ``approximate elongated isosceles triangle,'' ``approximate rectangle,'' and ``approximate cross'' are defined and used in the illustrative examples of this approach. By using these quantitative measures, a house, a house with high roof, and a church are also presented as illustrative examples. In addition, three fuzzy tree automata are constructed which have the capability of processing the fuzzy tree representations of ``fuzzy houses,'' ``houses with high roofs,'' and ``fuzzy churches,'' respectively. The results may have useful applications in pattern recognition, image processing, artificial intelligence, pattern database design and processing, image science, and pictorial information systems. PMID:21869062

  18. Learning fuzzy logic control system

    NASA Technical Reports Server (NTRS)

    Lung, Leung Kam

    1994-01-01

    The performance of the Learning Fuzzy Logic Control System (LFLCS), developed in this thesis, has been evaluated. The Learning Fuzzy Logic Controller (LFLC) learns to control the motor by learning the set of teaching values that are generated by a classical PI controller. It is assumed that the classical PI controller is tuned to minimize the error of a position control system of the D.C. motor. The Learning Fuzzy Logic Controller developed in this thesis is a multi-input single-output network. Training of the Learning Fuzzy Logic Controller is implemented off-line. Upon completion of the training process (using Supervised Learning, and Unsupervised Learning), the LFLC replaces the classical PI controller. In this thesis, a closed loop position control system of a D.C. motor using the LFLC is implemented. The primary focus is on the learning capabilities of the Learning Fuzzy Logic Controller. The learning includes symbolic representation of the Input Linguistic Nodes set and Output Linguistic Notes set. In addition, we investigate the knowledge-based representation for the network. As part of the design process, we implement a digital computer simulation of the LFLCS. The computer simulation program is written in 'C' computer language, and it is implemented in DOS platform. The LFLCS, designed in this thesis, has been developed on a IBM compatible 486-DX2 66 computer. First, the performance of the Learning Fuzzy Logic Controller is evaluated by comparing the angular shaft position of the D.C. motor controlled by a conventional PI controller and that controlled by the LFLC. Second, the symbolic representation of the LFLC and the knowledge-based representation for the network are investigated by observing the parameters of the Fuzzy Logic membership functions and the links at each layer of the LFLC. While there are some limitations of application with this approach, the result of the simulation shows that the LFLC is able to control the angular shaft position of the

  19. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing

    PubMed Central

    Sevim, Volkan; Bashir, Ali; Chin, Chen-Shan; Miga, Karen H.

    2016-01-01

    Motivation: Long arrays of near-identical tandem repeats are a common feature of centromeric and subtelomeric regions in complex genomes. These sequences present a source of repeat structure diversity that is commonly ignored by standard genomic tools. Unlike reads shorter than the underlying repeat structure that rely on indirect inference methods, e.g. assembly, long reads allow direct inference of satellite higher order repeat structure. To automate characterization of local centromeric tandem repeat sequence variation we have designed Alpha-CENTAURI (ALPHA satellite CENTromeric AUtomated Repeat Identification), that takes advantage of Pacific Bioscience long-reads from whole-genome sequencing datasets. By operating on reads prior to assembly, our approach provides a more comprehensive set of repeat-structure variants and is not impacted by rearrangements or sequence underrepresentation due to misassembly. Results: We demonstrate the utility of Alpha-CENTAURI in characterizing repeat structure for alpha satellite containing reads in the hydatidiform mole (CHM1, haploid-like) genome. The pipeline is designed to report local repeat organization summaries for each read, thereby monitoring rearrangements in repeat units, shifts in repeat orientation and sites of array transition into non-satellite DNA, typically defined by transposable element insertion. We validate the method by showing consistency with existing centromere high order repeat references. Alpha-CENTAURI can, in principle, run on any sequence data, offering a method to generate a sequence repeat resolution that could be readily performed using consensus sequences available for other satellite families in genomes without high-quality reference assemblies. Availability and implementation: Documentation and source code for Alpha-CENTAURI are freely available at http://github.com/volkansevim/alpha-CENTAURI. Contact: ali.bashir@mssm.edu Supplementary information: Supplementary data are available at

  20. Nanocrystal assembly for tandem catalysis

    DOEpatents

    Yang, Peidong; Somorjai, Gabor; Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu

    2014-10-14

    The present invention provides a nanocrystal tandem catalyst comprising at least two metal-metal oxide interfaces for the catalysis of sequential reactions. One embodiment utilizes a nanocrystal bilayer structure formed by assembling sub-10 nm platinum and cerium oxide nanocube monolayers on a silica substrate. The two distinct metal-metal oxide interfaces, CeO.sub.2--Pt and Pt--SiO.sub.2, can be used to catalyze two distinct sequential reactions. The CeO.sub.2--Pt interface catalyzed methanol decomposition to produce CO and H.sub.2, which were then subsequently used for ethylene hydroformylation catalyzed by the nearby Pt--SiO.sub.2 interface. Consequently, propanal was selectively produced on this nanocrystal bilayer tandem catalyst.

  1. Accumulate repeat accumulate codes

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

  2. Duct Leakage Repeatability Testing

    SciTech Connect

    Walker, Iain; Sherman, Max

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  3. "Nanocrystal bilayer for tandem catalysis"

    SciTech Connect

    Yamada, Yusuke; Tsung, Chia Kuang; Huang, Wenyu; Huo, Ziyang; E.Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Samorjai, Gabor A; Yang, Peidong

    2011-01-24

    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO2-Pt and Pt-SiO2, can be used to catalyse two distinct sequential reactions. The CeO2-Pt interface catalysed methanol decomposition to produce CO and H2, which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO2 interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts

  4. Combinational reasoning of quantitative fuzzy topological relations for simple fuzzy regions.

    PubMed

    Liu, Bo; Li, Dajun; Xia, Yuanping; Ruan, Jian; Xu, Lili; Wu, Huanyi

    2015-01-01

    In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computational fuzzy topological space is applied to simple fuzzy regions to efficiently and more accurately solve fuzzy topological relations. Thus, extending the existing research and improving upon the previous work, this paper presents a new method to describe fuzzy topological relations between simple spatial regions in Geographic Information Sciences (GIS) and Artificial Intelligence (AI). Firstly, we propose a new definition for simple fuzzy line segments and simple fuzzy regions based on the computational fuzzy topology. And then, based on the new definitions, we also propose a new combinational reasoning method to compute the topological relations between simple fuzzy regions, moreover, this study has discovered that there are (1) 23 different topological relations between a simple crisp region and a simple fuzzy region; (2) 152 different topological relations between two simple fuzzy regions. In the end, we have discussed some examples to demonstrate the validity of the new method, through comparisons with existing fuzzy models, we showed that the proposed method can compute more than the existing models, as it is more expressive than the existing fuzzy models. PMID:25775452

  5. Combinational Reasoning of Quantitative Fuzzy Topological Relations for Simple Fuzzy Regions

    PubMed Central

    Liu, Bo; Li, Dajun; Xia, Yuanping; Ruan, Jian; Xu, Lili; Wu, Huanyi

    2015-01-01

    In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computational fuzzy topological space is applied to simple fuzzy regions to efficiently and more accurately solve fuzzy topological relations. Thus, extending the existing research and improving upon the previous work, this paper presents a new method to describe fuzzy topological relations between simple spatial regions in Geographic Information Sciences (GIS) and Artificial Intelligence (AI). Firstly, we propose a new definition for simple fuzzy line segments and simple fuzzy regions based on the computational fuzzy topology. And then, based on the new definitions, we also propose a new combinational reasoning method to compute the topological relations between simple fuzzy regions, moreover, this study has discovered that there are (1) 23 different topological relations between a simple crisp region and a simple fuzzy region; (2) 152 different topological relations between two simple fuzzy regions. In the end, we have discussed some examples to demonstrate the validity of the new method, through comparisons with existing fuzzy models, we showed that the proposed method can compute more than the existing models, as it is more expressive than the existing fuzzy models. PMID:25775452

  6. Analysis of inventory difference using fuzzy controllers

    SciTech Connect

    Zardecki, A.

    1994-08-01

    The principal objectives of an accounting system for safeguarding nuclear materials are as follows: (a) to provide assurance that all material quantities are present in the correct amount; (b) to provide timely detection of material loss; and (c) to estimate the amount of any loss and its location. In fuzzy control, expert knowledge is encoded in the form of fuzzy rules, which describe recommended actions for different classes of situations represented by fuzzy sets. The concept of a fuzzy controller is applied to the forecasting problem in a time series, specifically, to forecasting and detecting anomalies in inventory differences. This paper reviews the basic notion underlying the fuzzy control systems and provides examples of application. The well-known material-unaccounted-for diffusion plant data of Jaech are analyzed using both feedforward neural networks and fuzzy controllers. By forming a deference between the forecasted and observed signals, an efficient method to detect small signals in background noise is implemented.

  7. (Fuzzy) Ideals of BN-Algebras

    PubMed Central

    Walendziak, Andrzej

    2015-01-01

    The notions of an ideal and a fuzzy ideal in BN-algebras are introduced. The properties and characterizations of them are investigated. The concepts of normal ideals and normal congruences of a BN-algebra are also studied, the properties of them are displayed, and a one-to-one correspondence between them is presented. Conditions for a fuzzy set to be a fuzzy ideal are given. The relationships between ideals and fuzzy ideals of a BN-algebra are established. The homomorphic properties of fuzzy ideals of a BN-algebra are provided. Finally, characterizations of Noetherian BN-algebras and Artinian BN-algebras via fuzzy ideals are obtained. PMID:26125050

  8. Predictive fuzzy controller for robotic motion control

    SciTech Connect

    Huang, S.J.; Hu, C.F.

    1995-12-31

    A system output prediction strategy incorporated with a fuzzy controller is proposed to manipulate the robotic motion control. Usually, the current position and velocity errors are used to operate the fuzzy logic controller for picking out a corresponding rule. When the system has fast planning speed or time varying behavior, the required tracking accuracy is difficult to achieve by adjusting the fuzzy rules. In order to improve the position control accuracy and system robustness for the industrial application, the current position error in the fuzzy rules look-up table is substituted by the predictive position error of the next step by using the grey predictive algorithm. This idea is implemented on a five degrees of freedom robot. The experimental results show that this fuzzy controller has effectively improve the system performance and achieved the facilitation of fuzzy controller implementation.

  9. Synthesis of hybrid bacterial plasmids containing highly repeated satellite DNA.

    PubMed

    Brutlag, D; Fry, K; Nelson, T; Hung, P

    1977-03-01

    Hybrid plasmid molecules containing tandemly repeated Drosophila satellite DNA were constructed using a modification of the (dA)-(dT) homopolymer procedure of Lobban and Kaiser (1973). Recombinant plasmids recovered after transformation of recA bacteria contained 10% of the amount of satellite DNA present in the transforming molecules. The cloned plasmids were not homogenous in size. Recombinant plasmids isolated from a single colony contained populations of circular molecules which varied both in the length of the satellite region and in the poly(dA)-(dt) regions linking satellite and vector. While subcloning reduced the heterogeneity of these plasmid populations, continued cell growth caused further variations in the size of the repeated regions. Two different simple sequence satellites of Drosophila melanogaster (1.672 and 1.705 g/cm3) were unstable in both recA and recBC hosts and in both pSC101 and pCR1 vectors. We propose that this recA-independent instability of tandemly repeated sequences is due to unequal intramolecular recombination events in replicating DNA molecules, a mechanism analogous to sister chromatid exchange in eucaryotes. PMID:403010

  10. Repeat-containing protein effectors of plant-associated organisms

    PubMed Central

    Mesarich, Carl H.; Bowen, Joanna K.; Hamiaux, Cyril; Templeton, Matthew D.

    2015-01-01

    Many plant-associated organisms, including microbes, nematodes, and insects, deliver effector proteins into the apoplast, vascular tissue, or cell cytoplasm of their prospective hosts. These effectors function to promote colonization, typically by altering host physiology or by modulating host immune responses. The same effectors however, can also trigger host immunity in the presence of cognate host immune receptor proteins, and thus prevent colonization. To circumvent effector-triggered immunity, or to further enhance host colonization, plant-associated organisms often rely on adaptive effector evolution. In recent years, it has become increasingly apparent that several effectors of plant-associated organisms are repeat-containing proteins (RCPs) that carry tandem or non-tandem arrays of an amino acid sequence or structural motif. In this review, we highlight the diverse roles that these repeat domains play in RCP effector function. We also draw attention to the potential role of these repeat domains in adaptive evolution with regards to RCP effector function and the evasion of effector-triggered immunity. The aim of this review is to increase the profile of RCP effectors from plant-associated organisms. PMID:26557126

  11. Fuzzy multiple linear regression: A computational approach

    NASA Technical Reports Server (NTRS)

    Juang, C. H.; Huang, X. H.; Fleming, J. W.

    1992-01-01

    This paper presents a new computational approach for performing fuzzy regression. In contrast to Bardossy's approach, the new approach, while dealing with fuzzy variables, closely follows the conventional regression technique. In this approach, treatment of fuzzy input is more 'computational' than 'symbolic.' The following sections first outline the formulation of the new approach, then deal with the implementation and computational scheme, and this is followed by examples to illustrate the new procedure.

  12. Fuzzy logic control for camera tracking system

    NASA Technical Reports Server (NTRS)

    Lea, Robert N.; Fritz, R. H.; Giarratano, J.; Jani, Yashvant

    1992-01-01

    A concept utilizing fuzzy theory has been developed for a camera tracking system to provide support for proximity operations and traffic management around the Space Station Freedom. Fuzzy sets and fuzzy logic based reasoning are used in a control system which utilizes images from a camera and generates required pan and tilt commands to track and maintain a moving target in the camera's field of view. This control system can be implemented on a fuzzy chip to provide an intelligent sensor for autonomous operations. Capabilities of the control system can be expanded to include approach, handover to other sensors, caution and warning messages.

  13. Refining fuzzy logic controllers with machine learning

    NASA Technical Reports Server (NTRS)

    Berenji, Hamid R.

    1994-01-01

    In this paper, we describe the GARIC (Generalized Approximate Reasoning-Based Intelligent Control) architecture, which learns from its past performance and modifies the labels in the fuzzy rules to improve performance. It uses fuzzy reinforcement learning which is a hybrid method of fuzzy logic and reinforcement learning. This technology can simplify and automate the application of fuzzy logic control to a variety of systems. GARIC has been applied in simulation studies of the Space Shuttle rendezvous and docking experiments. It has the potential of being applied in other aerospace systems as well as in consumer products such as appliances, cameras, and cars.

  14. Fuzzy control of small servo motors

    NASA Technical Reports Server (NTRS)

    Maor, Ron; Jani, Yashvant

    1993-01-01

    To explore the benefits of fuzzy logic and understand the differences between the classical control methods and fuzzy control methods, the Togai InfraLogic applications engineering staff developed and implemented a motor control system for small servo motors. The motor assembly for testing the fuzzy and conventional controllers consist of servo motor RA13M and an encoder with a range of 4096 counts. An interface card was designed and fabricated to interface the motor assembly and encoder to an IBM PC. The fuzzy logic based motor controller was developed using the TILShell and Fuzzy C Development System on an IBM PC. A Proportional-Derivative (PD) type conventional controller was also developed and implemented in the IBM PC to compare the performance with the fuzzy controller. Test cases were defined to include step inputs of 90 and 180 degrees rotation, sine and square wave profiles in 5 to 20 hertz frequency range, as well as ramp inputs. In this paper we describe our approach to develop a fuzzy as well as PH controller, provide details of hardware set-up and test cases, and discuss the performance results. In comparison, the fuzzy logic based controller handles the non-linearities of the motor assembly very well and provides excellent control over a broad range of parameters. Fuzzy technology, as indicated by our results, possesses inherent adaptive features.

  15. Fuzzy logic control and optimization system

    DOEpatents

    Lou, Xinsheng

    2012-04-17

    A control system (300) for optimizing a power plant includes a chemical loop having an input for receiving an input signal (369) and an output for outputting an output signal (367), and a hierarchical fuzzy control system (400) operably connected to the chemical loop. The hierarchical fuzzy control system (400) includes a plurality of fuzzy controllers (330). The hierarchical fuzzy control system (400) receives the output signal (367), optimizes the input signal (369) based on the received output signal (367), and outputs an optimized input signal (369) to the input of the chemical loop to control a process of the chemical loop in an optimized manner.

  16. A fuzzy classifier system for process control

    NASA Technical Reports Server (NTRS)

    Karr, C. L.; Phillips, J. C.

    1994-01-01

    A fuzzy classifier system that discovers rules for controlling a mathematical model of a pH titration system was developed by researchers at the U.S. Bureau of Mines (USBM). Fuzzy classifier systems successfully combine the strengths of learning classifier systems and fuzzy logic controllers. Learning classifier systems resemble familiar production rule-based systems, but they represent their IF-THEN rules by strings of characters rather than in the traditional linguistic terms. Fuzzy logic is a tool that allows for the incorporation of abstract concepts into rule based-systems, thereby allowing the rules to resemble the familiar 'rules-of-thumb' commonly used by humans when solving difficult process control and reasoning problems. Like learning classifier systems, fuzzy classifier systems employ a genetic algorithm to explore and sample new rules for manipulating the problem environment. Like fuzzy logic controllers, fuzzy classifier systems encapsulate knowledge in the form of production rules. The results presented in this paper demonstrate the ability of fuzzy classifier systems to generate a fuzzy logic-based process control system.

  17. Fuzzy set classifier for waste classification tracking

    SciTech Connect

    Gavel, D.T.

    1992-11-04

    We have developed an expert system based on fuzzy logic theory to fuse the data from multiple sensors and make classification decisions for objects in a waste reprocessing stream. Fuzzy set theory has been applied in decision and control applications with some success, particularly by the Japanese. We have found that the fuzzy logic system is rather easy to design and train, a feature that can cut development costs considerably. With proper training, the classification accuracy is quite high. We performed several tests sorting radioactive test samples using a gamma spectrometer to compare fuzzy logic to more conventional sorting schemes.

  18. Indirect Adaptive Fuzzy Power System Stabilizer

    NASA Astrophysics Data System (ADS)

    Saoudi, Kamel; Bouchama, Ziad; Harmas, Mohamed Naguib; Zehar, Khaled

    2008-06-01

    A power system stabilizer based on adaptive fuzzy technique is presented. The design of a fuzzy logic power system stabilizer (FLPSS) requires the collection of fuzzy IF-THEN rules which are used to initialize an adaptive fuzzy power system AFPSS. The rule-base can be then tuned on-line so that the stabilizer can adapt to the different operating conditions occurring in the power system. The adaptation laws are developed based on a Lyapunov synthesis approach. Assessing the validity of this technique simulation of a power system is conducted and results are discussed.

  19. The characterization of tandem and corrugated wings